Diff of the two buildlogs: -- --- b1/build.log 2024-05-06 14:59:53.851750076 +0000 +++ b2/build.log 2024-05-06 15:03:49.377727587 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 8 09:21:11 -12 2025 -I: pbuilder-time-stamp: 1749417671 +I: Current time: Tue May 7 04:59:56 +14 2024 +I: pbuilder-time-stamp: 1715007596 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking libpwizlite_3.0.5-2.1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/805881/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 6 15:00 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1b01fa717e774a589ed55730883ddfe2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='805881' - PS1='# ' - PS2='> ' + INVOCATION_ID=5d9418982a9345ef98569f80644d8782 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3373538 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jL2GOwKL/pbuilderrc_6qG9 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jL2GOwKL/b1 --logfile b1/build.log libpwizlite_3.0.5-2.1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jL2GOwKL/pbuilderrc_7HD1 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jL2GOwKL/b2 --logfile b2/build.log libpwizlite_3.0.5-2.1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/805881/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 3 08:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -222,7 +254,7 @@ Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-roman all 3.3-3 [9880 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] -Fetched 68.7 MB in 1s (78.2 MB/s) +Fetched 68.7 MB in 1s (48.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19698 files and directories currently installed.) @@ -558,8 +590,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jun 8 21:21:59 UTC 2025. -Universal Time is now: Sun Jun 8 21:21:59 UTC 2025. +Local time is now: Mon May 6 15:01:34 UTC 2024. +Universal Time is now: Mon May 6 15:01:34 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-2.1+b1) ... @@ -648,7 +680,11 @@ fakeroot is already the newest version (1.33-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libpwizlite-3.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libpwizlite_3.0.5-2.1_source.changes +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3373538/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpwizlite-3.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libpwizlite_3.0.5-2.1_source.changes dpkg-buildpackage: info: source package libpwizlite dpkg-buildpackage: info: source version 3.0.5-2.1 dpkg-buildpackage: info: source distribution unstable @@ -721,7 +757,7 @@ -- Boost_INCLUDES: /usr/include -- Boost_LIB_DIRS: /usr/lib/x86_64-linux-gnu STATUS: Now managing the CPack process --- Configuring done (0.6s) +-- Configuring done (2.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -734,390 +770,459 @@ -- Build files have been written to: /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu rst2man debian/libpwizlite.3.rst > debian/libpwizlite.3 sh debian/make-included-headers-hierarchy.sh +baseName: convert.hpp +dirName: boost/nowide +'boost/nowide/convert.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/convert.hpp' +baseName: args.hpp +dirName: boost/nowide +'boost/nowide/args.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/args.hpp' +baseName: windows.hpp +dirName: boost/nowide +'boost/nowide/windows.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/windows.hpp' +baseName: config.hpp +dirName: boost/nowide +'boost/nowide/config.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/config.hpp' +baseName: iostream.hpp +dirName: boost/nowide +'boost/nowide/iostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/iostream.hpp' +baseName: cenv.hpp +dirName: boost/nowide +'boost/nowide/cenv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cenv.hpp' +baseName: cstdlib.hpp +dirName: boost/nowide +'boost/nowide/cstdlib.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cstdlib.hpp' +baseName: cstdio.hpp +dirName: boost/nowide +'boost/nowide/cstdio.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cstdio.hpp' +baseName: system.hpp +dirName: boost/nowide +'boost/nowide/system.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/system.hpp' +baseName: stackstring.hpp +dirName: boost/nowide +'boost/nowide/stackstring.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/stackstring.hpp' +baseName: filebuf.hpp +dirName: boost/nowide +'boost/nowide/filebuf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/filebuf.hpp' +baseName: fstream.hpp +dirName: boost/nowide +'boost/nowide/fstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/fstream.hpp' +baseName: macros.hpp +dirName: boost/enum +'boost/enum/macros.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/macros.hpp' +baseName: bitfield.hpp +dirName: boost/enum +'boost/enum/bitfield.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/bitfield.hpp' baseName: base.hpp -dirName: pwiz/utility/findmf/base/base/utilities -'pwiz/utility/findmf/base/base/utilities/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/base.hpp' -baseName: interpolation.hpp -dirName: pwiz/utility/findmf/base/base/utilities -'pwiz/utility/findmf/base/base/utilities/interpolation.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/interpolation.hpp' -baseName: constants.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/constants.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/constants.hpp' -baseName: interpolate.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/interpolate.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/interpolate.hpp' -baseName: base.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/base.hpp' -baseName: scale.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/scale.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/scale.hpp' -baseName: copyif.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/copyif.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/copyif.hpp' -baseName: diff.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/diff.hpp' -baseName: determinebinwidth.hpp -dirName: pwiz/utility/findmf/base/resample/utilities -'pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -baseName: masscomparefunctors.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -baseName: breakspec.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/breakspec.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/breakspec.hpp' -baseName: determinebinwidth.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/determinebinwidth.hpp' -baseName: bin1d.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/bin1d.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/bin1d.hpp' -baseName: preparedata.hpp -dirName: pwiz/utility/findmf/base/filter/utilities -'pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -baseName: gauss.hpp -dirName: pwiz/utility/findmf/base/filter/utilities -'pwiz/utility/findmf/base/filter/utilities/gauss.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/gauss.hpp' -baseName: gaussfilter.hpp -dirName: pwiz/utility/findmf/base/filter -'pwiz/utility/findmf/base/filter/gaussfilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/gaussfilter.hpp' -baseName: filter.hpp -dirName: pwiz/utility/findmf/base/filter -'pwiz/utility/findmf/base/filter/filter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/filter.hpp' -baseName: SAXParser.hpp -dirName: pwiz/utility/minimxml -'pwiz/utility/minimxml/SAXParser.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/minimxml/SAXParser.hpp' +dirName: boost/enum +'boost/enum/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/base.hpp' +baseName: iterator.hpp +dirName: boost/enum +'boost/enum/iterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/iterator.hpp' +baseName: singleton.hpp +dirName: boost/utility +'boost/utility/singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/singleton.hpp' +baseName: singleton_manager.hpp +dirName: boost/utility/detail +'boost/utility/detail/singleton_manager.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/singleton_manager.hpp' +baseName: member_dereference.hpp +dirName: boost/utility/detail +'boost/utility/detail/member_dereference.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/member_dereference.hpp' +baseName: restricted.hpp +dirName: boost/utility/detail +'boost/utility/detail/restricted.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/restricted.hpp' +baseName: thread_specific_singleton.hpp +dirName: boost/utility +'boost/utility/thread_specific_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/thread_specific_singleton.hpp' +baseName: mutexed_singleton.hpp +dirName: boost/utility +'boost/utility/mutexed_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/mutexed_singleton.hpp' +baseName: enum.hpp +dirName: boost +'boost/enum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum.hpp' +baseName: foreach_field.hpp +dirName: boost +'boost/foreach_field.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/foreach_field.hpp' +baseName: base64.hpp +dirName: boost/iostreams/filter +'boost/iostreams/filter/base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/iostreams/filter/base64.hpp' +baseName: arbitrary_positional_facade.hpp +dirName: boost/iostreams +'boost/iostreams/arbitrary_positional_facade.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/iostreams/arbitrary_positional_facade.hpp' +baseName: Version.hpp +dirName: pwiz +'pwiz/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/Version.hpp' +baseName: IsotopeCalculator.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeCalculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeCalculator.hpp' +baseName: Chemistry.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/Chemistry.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/Chemistry.hpp' +baseName: MzMobilityWindow.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/MzMobilityWindow.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/MzMobilityWindow.hpp' +baseName: ChemistryData.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/ChemistryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/ChemistryData.hpp' +baseName: Ion.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/Ion.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/Ion.hpp' +baseName: MZTolerance.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/MZTolerance.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/MZTolerance.hpp' +baseName: IsotopeEnvelopeEstimator.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' +baseName: IsotopeTable.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeTable.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeTable.hpp' baseName: XMLWriter.hpp dirName: pwiz/utility/minimxml 'pwiz/utility/minimxml/XMLWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/minimxml/XMLWriter.hpp' -baseName: round.hpp +baseName: SAXParser.hpp +dirName: pwiz/utility/minimxml +'pwiz/utility/minimxml/SAXParser.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/minimxml/SAXParser.hpp' +baseName: Stats.hpp dirName: pwiz/utility/math -'pwiz/utility/math/round.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/round.hpp' +'pwiz/utility/math/Stats.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Stats.hpp' baseName: OrderedPair.hpp dirName: pwiz/utility/math 'pwiz/utility/math/OrderedPair.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/OrderedPair.hpp' +baseName: qr.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/qr.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/qr.hpp' baseName: MatrixInverse.hpp dirName: pwiz/utility/math 'pwiz/utility/math/MatrixInverse.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/MatrixInverse.hpp' +baseName: Types.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/Types.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Types.hpp' baseName: HouseholderQR.hpp dirName: pwiz/utility/math 'pwiz/utility/math/HouseholderQR.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/HouseholderQR.hpp' -baseName: erf.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/erf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/erf.hpp' -baseName: qr.hpp +baseName: LinearLeastSquares.hpp dirName: pwiz/utility/math -'pwiz/utility/math/qr.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/qr.hpp' +'pwiz/utility/math/LinearLeastSquares.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/LinearLeastSquares.hpp' baseName: LinearSolver.hpp dirName: pwiz/utility/math 'pwiz/utility/math/LinearSolver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/LinearSolver.hpp' -baseName: Parabola.hpp +baseName: erf.hpp dirName: pwiz/utility/math -'pwiz/utility/math/Parabola.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Parabola.hpp' +'pwiz/utility/math/erf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/erf.hpp' baseName: MatchedFilter.hpp dirName: pwiz/utility/math 'pwiz/utility/math/MatchedFilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/MatchedFilter.hpp' -baseName: Stats.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/Stats.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Stats.hpp' -baseName: LinearLeastSquares.hpp +baseName: round.hpp dirName: pwiz/utility/math -'pwiz/utility/math/LinearLeastSquares.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/LinearLeastSquares.hpp' -baseName: Types.hpp +'pwiz/utility/math/round.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/round.hpp' +baseName: Parabola.hpp dirName: pwiz/utility/math -'pwiz/utility/math/Types.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Types.hpp' -baseName: Ion.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/Ion.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/Ion.hpp' -baseName: IsotopeEnvelopeEstimator.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -baseName: MZTolerance.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/MZTolerance.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/MZTolerance.hpp' -baseName: MzMobilityWindow.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/MzMobilityWindow.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/MzMobilityWindow.hpp' -baseName: IsotopeCalculator.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeCalculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeCalculator.hpp' -baseName: ChemistryData.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/ChemistryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/ChemistryData.hpp' -baseName: IsotopeTable.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeTable.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeTable.hpp' -baseName: Chemistry.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/Chemistry.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/chemistry/Chemistry.hpp' +'pwiz/utility/math/Parabola.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/math/Parabola.hpp' +baseName: scale.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/scale.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/scale.hpp' +baseName: interpolation.hpp +dirName: pwiz/utility/findmf/base/base/utilities +'pwiz/utility/findmf/base/base/utilities/interpolation.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/interpolation.hpp' +baseName: base.hpp +dirName: pwiz/utility/findmf/base/base/utilities +'pwiz/utility/findmf/base/base/utilities/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/base.hpp' +baseName: copyif.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/copyif.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/copyif.hpp' +baseName: constants.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/constants.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/constants.hpp' +baseName: diff.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/diff.hpp' +baseName: base.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/base.hpp' +baseName: interpolate.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/interpolate.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/base/interpolate.hpp' +baseName: filter.hpp +dirName: pwiz/utility/findmf/base/filter +'pwiz/utility/findmf/base/filter/filter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/filter.hpp' +baseName: gauss.hpp +dirName: pwiz/utility/findmf/base/filter/utilities +'pwiz/utility/findmf/base/filter/utilities/gauss.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/gauss.hpp' +baseName: preparedata.hpp +dirName: pwiz/utility/findmf/base/filter/utilities +'pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' +baseName: gaussfilter.hpp +dirName: pwiz/utility/findmf/base/filter +'pwiz/utility/findmf/base/filter/gaussfilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/gaussfilter.hpp' +baseName: bin1d.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/bin1d.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/bin1d.hpp' +baseName: determinebinwidth.hpp +dirName: pwiz/utility/findmf/base/resample/utilities +'pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' +baseName: breakspec.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/breakspec.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/breakspec.hpp' +baseName: determinebinwidth.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/determinebinwidth.hpp' +baseName: masscomparefunctors.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' +baseName: unit.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/unit.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/unit.hpp' baseName: TabReader.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/TabReader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/TabReader.hpp' -baseName: endian.hpp +baseName: Stream.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/endian.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/endian.hpp' +'pwiz/utility/misc/Stream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Stream.hpp' baseName: Environment.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/Environment.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Environment.hpp' -baseName: BinaryData.hpp +baseName: Base64.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/BinaryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/BinaryData.hpp' -baseName: IntegerSet.hpp +'pwiz/utility/misc/Base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Base64.hpp' +baseName: Singleton.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/IntegerSet.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/IntegerSet.hpp' -baseName: CharIndexedVector.hpp +'pwiz/utility/misc/Singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Singleton.hpp' +baseName: optimized_lexical_cast.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/CharIndexedVector.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/CharIndexedVector.hpp' -baseName: SHA1Calculator.hpp +'pwiz/utility/misc/optimized_lexical_cast.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/optimized_lexical_cast.hpp' +baseName: Std.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/SHA1Calculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/SHA1Calculator.hpp' -baseName: almost_equal.hpp +'pwiz/utility/misc/Std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Std.hpp' +baseName: Image.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/almost_equal.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/almost_equal.hpp' -baseName: automation_vector.h +'pwiz/utility/misc/Image.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Image.hpp' +baseName: MSIHandler.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/automation_vector.h' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/automation_vector.h' -baseName: Container.hpp +'pwiz/utility/misc/MSIHandler.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/MSIHandler.hpp' +baseName: Filesystem.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Container.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Container.hpp' -baseName: optimized_lexical_cast.hpp +'pwiz/utility/misc/Filesystem.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Filesystem.hpp' +baseName: IntegerSet.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/optimized_lexical_cast.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/optimized_lexical_cast.hpp' -baseName: Exception.hpp +'pwiz/utility/misc/IntegerSet.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/IntegerSet.hpp' +baseName: Container.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Exception.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Exception.hpp' -baseName: shared_map.hpp +'pwiz/utility/misc/Container.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Container.hpp' +baseName: CharIndexedVector.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/shared_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/shared_map.hpp' +'pwiz/utility/misc/CharIndexedVector.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/CharIndexedVector.hpp' baseName: VendorReaderTestHarness.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/VendorReaderTestHarness.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/VendorReaderTestHarness.hpp' -baseName: mru_list.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/mru_list.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/mru_list.hpp' -baseName: Export.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/Export.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Export.hpp' -baseName: SHA1_ostream.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/SHA1_ostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/SHA1_ostream.hpp' -baseName: MSIHandler.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/MSIHandler.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/MSIHandler.hpp' -baseName: virtual_map.hpp +baseName: Once.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/virtual_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/virtual_map.hpp' +'pwiz/utility/misc/Once.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Once.hpp' baseName: IterationListener.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/IterationListener.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/IterationListener.hpp' -baseName: random_access_compressed_ifstream.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/random_access_compressed_ifstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/random_access_compressed_ifstream.hpp' -baseName: Image.hpp +baseName: Exception.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Image.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Image.hpp' -baseName: unit.hpp +'pwiz/utility/misc/Exception.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Exception.hpp' +baseName: BinaryData.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/unit.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/unit.hpp' -baseName: Stream.hpp +'pwiz/utility/misc/BinaryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/BinaryData.hpp' +baseName: SHA1Calculator.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Stream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Stream.hpp' -baseName: Filesystem.hpp +'pwiz/utility/misc/SHA1Calculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/SHA1Calculator.hpp' +baseName: Timer.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Filesystem.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Filesystem.hpp' -baseName: COMInitializer.hpp +'pwiz/utility/misc/Timer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Timer.hpp' +baseName: virtual_map.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/COMInitializer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/COMInitializer.hpp' -baseName: Std.hpp +'pwiz/utility/misc/virtual_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/virtual_map.hpp' +baseName: shared_map.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Std.hpp' +'pwiz/utility/misc/shared_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/shared_map.hpp' baseName: SHA1.h dirName: pwiz/utility/misc 'pwiz/utility/misc/SHA1.h' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/SHA1.h' -baseName: cpp_cli_utilities.hpp +baseName: SHA1_ostream.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/cpp_cli_utilities.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/cpp_cli_utilities.hpp' -baseName: Timer.hpp +'pwiz/utility/misc/SHA1_ostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/SHA1_ostream.hpp' +baseName: random_access_compressed_ifstream.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Timer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Timer.hpp' +'pwiz/utility/misc/random_access_compressed_ifstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/random_access_compressed_ifstream.hpp' baseName: String.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/String.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/String.hpp' -baseName: Base64.hpp +baseName: endian.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Base64.hpp' -baseName: Once.hpp +'pwiz/utility/misc/endian.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/endian.hpp' +baseName: automation_vector.h dirName: pwiz/utility/misc -'pwiz/utility/misc/Once.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Once.hpp' +'pwiz/utility/misc/automation_vector.h' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/automation_vector.h' +baseName: cpp_cli_utilities.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/cpp_cli_utilities.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/cpp_cli_utilities.hpp' baseName: ClickwrapPrompter.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/ClickwrapPrompter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/ClickwrapPrompter.hpp' -baseName: Singleton.hpp +baseName: mru_list.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Singleton.hpp' +'pwiz/utility/misc/mru_list.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/mru_list.hpp' +baseName: almost_equal.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/almost_equal.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/almost_equal.hpp' +baseName: Export.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/Export.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/Export.hpp' +baseName: COMInitializer.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/COMInitializer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/COMInitializer.hpp' baseName: DateTime.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/DateTime.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/utility/misc/DateTime.hpp' -baseName: SpectrumList_Demux.hpp -dirName: pwiz/analysis/spectrum_processing -'pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' -baseName: DemuxDataProcessingStrings.hpp -dirName: pwiz/analysis/demux -'pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' baseName: Version.hpp -dirName: pwiz -'pwiz/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/Version.hpp' -baseName: Index.hpp -dirName: pwiz/data/common -'pwiz/data/common/Index.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/Index.hpp' -baseName: obo.hpp -dirName: pwiz/data/common -'pwiz/data/common/obo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/obo.hpp' -baseName: CVTranslator.hpp -dirName: pwiz/data/common -'pwiz/data/common/CVTranslator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/CVTranslator.hpp' -baseName: MemoryIndex.hpp -dirName: pwiz/data/common -'pwiz/data/common/MemoryIndex.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/MemoryIndex.hpp' -baseName: cv.hpp -dirName: pwiz/data/common -'pwiz/data/common/cv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/cv.hpp' -baseName: BinaryIndexStream.hpp -dirName: pwiz/data/common -'pwiz/data/common/BinaryIndexStream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/BinaryIndexStream.hpp' -baseName: Unimod.hpp -dirName: pwiz/data/common -'pwiz/data/common/Unimod.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/Unimod.hpp' -baseName: diff_std.hpp -dirName: pwiz/data/common -'pwiz/data/common/diff_std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/diff_std.hpp' -baseName: ParamTypes.hpp -dirName: pwiz/data/common -'pwiz/data/common/ParamTypes.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/ParamTypes.hpp' -baseName: SHA1OutputObserver.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SHA1OutputObserver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SHA1OutputObserver.hpp' -baseName: IO.hpp +'pwiz/data/msdata/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Version.hpp' +baseName: Serializer_MGF.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/IO.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/IO.hpp' +'pwiz/data/msdata/Serializer_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MGF.hpp' +baseName: SpectrumWorkerThreads.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumWorkerThreads.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumWorkerThreads.hpp' baseName: SpectrumListCache.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/SpectrumListCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListCache.hpp' -baseName: DefaultReaderList.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/DefaultReaderList.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/DefaultReaderList.hpp' -baseName: examples.hpp +baseName: SpectrumListBase.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/examples.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/examples.hpp' -baseName: References.hpp +'pwiz/data/msdata/SpectrumListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListBase.hpp' +baseName: Serializer_mzXML.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/References.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/References.hpp' -baseName: BinaryDataEncoder.hpp +'pwiz/data/msdata/Serializer_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzXML.hpp' +baseName: Diff.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/BinaryDataEncoder.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/BinaryDataEncoder.hpp' +'pwiz/data/msdata/Diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Diff.hpp' baseName: RAMPAdapter.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/RAMPAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/RAMPAdapter.hpp' -baseName: Reader.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Reader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Reader.hpp' -baseName: Serializer_mz5.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mz5.hpp' -baseName: SpectrumIterator.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumIterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumIterator.hpp' -baseName: MemoryMRUCache.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MemoryMRUCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MemoryMRUCache.hpp' -baseName: Serializer_MGF.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MGF.hpp' -baseName: SpectrumList_mzML.hpp +baseName: ChromatogramList_mz5.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzML.hpp' +'pwiz/data/msdata/ChromatogramList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mz5.hpp' baseName: SpectrumList_MSn.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/SpectrumList_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MSn.hpp' -baseName: Serializer_mzXML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzXML.hpp' -baseName: ChromatogramListBase.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/ChromatogramListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramListBase.hpp' baseName: MSDataFile.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/MSDataFile.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSDataFile.hpp' baseName: MSData.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/MSData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSData.hpp' -baseName: SpectrumList_mzXML.hpp +baseName: SpectrumList_MGF.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzXML.hpp' +'pwiz/data/msdata/SpectrumList_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MGF.hpp' +baseName: ChromatogramListBase.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/ChromatogramListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramListBase.hpp' +baseName: References.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/References.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/References.hpp' baseName: SpectrumInfo.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/SpectrumInfo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumInfo.hpp' -baseName: MSDataMerger.hpp +baseName: MSNumpress.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/MSDataMerger.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSDataMerger.hpp' -baseName: SpectrumList_BTDX.hpp +'pwiz/data/msdata/MSNumpress.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSNumpress.hpp' +baseName: LegacyAdapter.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_BTDX.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_BTDX.hpp' -baseName: Diff.hpp +'pwiz/data/msdata/LegacyAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/LegacyAdapter.hpp' +baseName: Reader.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/Diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Diff.hpp' -baseName: SpectrumList_MGF.hpp +'pwiz/data/msdata/Reader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Reader.hpp' +baseName: DefaultReaderList.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MGF.hpp' -baseName: SpectrumWorkerThreads.hpp +'pwiz/data/msdata/DefaultReaderList.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/DefaultReaderList.hpp' +baseName: Serializer_mz5.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumWorkerThreads.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumWorkerThreads.hpp' +'pwiz/data/msdata/Serializer_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mz5.hpp' +baseName: SpectrumList_mzXML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzXML.hpp' baseName: SpectrumListWrapper.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/SpectrumListWrapper.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListWrapper.hpp' +baseName: IO.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/IO.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/IO.hpp' +baseName: SpectrumList_BTDX.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_BTDX.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_BTDX.hpp' baseName: Serializer_MSn.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/Serializer_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MSn.hpp' baseName: SpectrumList_mz5.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/SpectrumList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mz5.hpp' -baseName: ChromatogramList_mz5.hpp +baseName: SpectrumIterator.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/ChromatogramList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mz5.hpp' +'pwiz/data/msdata/SpectrumIterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumIterator.hpp' baseName: Serializer_mzML.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/Serializer_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzML.hpp' -baseName: SpectrumListBase.hpp +baseName: SpectrumList_mzML.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListBase.hpp' -baseName: Version.hpp +'pwiz/data/msdata/SpectrumList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzML.hpp' +baseName: examples.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Version.hpp' -baseName: LegacyAdapter.hpp +'pwiz/data/msdata/examples.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/examples.hpp' +baseName: SHA1OutputObserver.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/LegacyAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/LegacyAdapter.hpp' +'pwiz/data/msdata/SHA1OutputObserver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/SHA1OutputObserver.hpp' +baseName: MemoryMRUCache.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MemoryMRUCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MemoryMRUCache.hpp' baseName: Index_mzML.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/Index_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/Index_mzML.hpp' -baseName: MSNumpress.hpp +baseName: MSDataMerger.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/MSNumpress.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSNumpress.hpp' -baseName: TextWriter.hpp +'pwiz/data/msdata/MSDataMerger.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/MSDataMerger.hpp' +baseName: BinaryDataEncoder.hpp dirName: pwiz/data/msdata -'pwiz/data/msdata/TextWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/TextWriter.hpp' +'pwiz/data/msdata/BinaryDataEncoder.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/BinaryDataEncoder.hpp' baseName: ChromatogramList_mzML.hpp dirName: pwiz/data/msdata 'pwiz/data/msdata/ChromatogramList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mzML.hpp' -baseName: CalibrationParameters.hpp +baseName: TextWriter.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/TextWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/msdata/TextWriter.hpp' +baseName: Index.hpp +dirName: pwiz/data/common +'pwiz/data/common/Index.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/Index.hpp' +baseName: MemoryIndex.hpp +dirName: pwiz/data/common +'pwiz/data/common/MemoryIndex.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/MemoryIndex.hpp' +baseName: BinaryIndexStream.hpp +dirName: pwiz/data/common +'pwiz/data/common/BinaryIndexStream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/BinaryIndexStream.hpp' +baseName: obo.hpp +dirName: pwiz/data/common +'pwiz/data/common/obo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/obo.hpp' +baseName: diff_std.hpp +dirName: pwiz/data/common +'pwiz/data/common/diff_std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/diff_std.hpp' +baseName: Unimod.hpp +dirName: pwiz/data/common +'pwiz/data/common/Unimod.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/Unimod.hpp' +baseName: cv.hpp +dirName: pwiz/data/common +'pwiz/data/common/cv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/cv.hpp' +baseName: ParamTypes.hpp +dirName: pwiz/data/common +'pwiz/data/common/ParamTypes.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/ParamTypes.hpp' +baseName: CVTranslator.hpp +dirName: pwiz/data/common +'pwiz/data/common/CVTranslator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/common/CVTranslator.hpp' +baseName: FrequencyData.hpp dirName: pwiz/data/misc -'pwiz/data/misc/CalibrationParameters.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/CalibrationParameters.hpp' +'pwiz/data/misc/FrequencyData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/FrequencyData.hpp' baseName: MinimumPepXML.hpp dirName: pwiz/data/misc 'pwiz/data/misc/MinimumPepXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/MinimumPepXML.hpp' -baseName: FrequencyData.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/FrequencyData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/FrequencyData.hpp' baseName: PeakData.hpp dirName: pwiz/data/misc 'pwiz/data/misc/PeakData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/PeakData.hpp' @@ -1127,87 +1232,18 @@ baseName: SampleDatum.hpp dirName: pwiz/data/misc 'pwiz/data/misc/SampleDatum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/SampleDatum.hpp' -baseName: mutexed_singleton.hpp -dirName: boost/utility -'boost/utility/mutexed_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/mutexed_singleton.hpp' -baseName: thread_specific_singleton.hpp -dirName: boost/utility -'boost/utility/thread_specific_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/thread_specific_singleton.hpp' -baseName: member_dereference.hpp -dirName: boost/utility/detail -'boost/utility/detail/member_dereference.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/member_dereference.hpp' -baseName: singleton_manager.hpp -dirName: boost/utility/detail -'boost/utility/detail/singleton_manager.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/singleton_manager.hpp' -baseName: restricted.hpp -dirName: boost/utility/detail -'boost/utility/detail/restricted.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/detail/restricted.hpp' -baseName: singleton.hpp -dirName: boost/utility -'boost/utility/singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/utility/singleton.hpp' -baseName: args.hpp -dirName: boost/nowide -'boost/nowide/args.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/args.hpp' -baseName: filebuf.hpp -dirName: boost/nowide -'boost/nowide/filebuf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/filebuf.hpp' -baseName: convert.hpp -dirName: boost/nowide -'boost/nowide/convert.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/convert.hpp' -baseName: cstdio.hpp -dirName: boost/nowide -'boost/nowide/cstdio.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cstdio.hpp' -baseName: cstdlib.hpp -dirName: boost/nowide -'boost/nowide/cstdlib.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cstdlib.hpp' -baseName: config.hpp -dirName: boost/nowide -'boost/nowide/config.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/config.hpp' -baseName: stackstring.hpp -dirName: boost/nowide -'boost/nowide/stackstring.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/stackstring.hpp' -baseName: windows.hpp -dirName: boost/nowide -'boost/nowide/windows.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/windows.hpp' -baseName: fstream.hpp -dirName: boost/nowide -'boost/nowide/fstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/fstream.hpp' -baseName: system.hpp -dirName: boost/nowide -'boost/nowide/system.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/system.hpp' -baseName: iostream.hpp -dirName: boost/nowide -'boost/nowide/iostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/iostream.hpp' -baseName: cenv.hpp -dirName: boost/nowide -'boost/nowide/cenv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/nowide/cenv.hpp' -baseName: macros.hpp -dirName: boost/enum -'boost/enum/macros.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/macros.hpp' -baseName: iterator.hpp -dirName: boost/enum -'boost/enum/iterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/iterator.hpp' -baseName: bitfield.hpp -dirName: boost/enum -'boost/enum/bitfield.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/bitfield.hpp' -baseName: base.hpp -dirName: boost/enum -'boost/enum/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum/base.hpp' -baseName: foreach_field.hpp -dirName: boost -'boost/foreach_field.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/foreach_field.hpp' -baseName: base64.hpp -dirName: boost/iostreams/filter -'boost/iostreams/filter/base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/iostreams/filter/base64.hpp' -baseName: arbitrary_positional_facade.hpp -dirName: boost/iostreams -'boost/iostreams/arbitrary_positional_facade.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/iostreams/arbitrary_positional_facade.hpp' -baseName: enum.hpp -dirName: boost -'boost/enum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/boost/enum.hpp' +baseName: CalibrationParameters.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/CalibrationParameters.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/data/misc/CalibrationParameters.hpp' +baseName: DemuxDataProcessingStrings.hpp +dirName: pwiz/analysis/demux +'pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' +baseName: SpectrumList_Demux.hpp +dirName: pwiz/analysis/spectrum_processing +'pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' -> '/build/reproducible-path/libpwizlite-3.0.5/debian/includes/pwizlite/pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' make[1]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.5' dh_auto_build -O--build-system=cmake - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libpwizlite-3.0.5 -B/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1216,109 +1252,55 @@ make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/depend make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.5 /build/reproducible-path/libpwizlite-3.0.5/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-static.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.5 /build/reproducible-path/libpwizlite-3.0.5/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-shared.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/build +make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.5 /build/reproducible-path/libpwizlite-3.0.5/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-static.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/build +make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/build make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu' -[ 1%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -[ 3%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o -[ 3%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -[ 5%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -[ 6%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -[ 8%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -[ 8%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -[ 10%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -[ 12%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o -[ 12%] Building 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object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.cpp +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Base64.cpp +[ 15%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o +[ 15%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o +[ 15%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o +[ 15%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp -[ 51%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Version.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp -[ 52%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 114 | } else if (init == mask) { - | ~~~~~^~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 114 | } else if (init == mask) { - | ~~~~~^~~~~~~ -[ 53%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +[ 23%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +[ 25%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/SHA1Calculator.cpp +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/SHA1Calculator.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined 54 | #pragma GCC warning "WIN32 is NOT defined" | ^~~~~~~~~~~~~~~~~~~~~~ @@ -1354,215 +1336,9 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:27: -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:403:33: -/usr/include/c++/13/ostream:204:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] - 204 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here - 346 | long long extrapol; - | ^~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:404:26: -/usr/include/c++/13/ostream:204:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] - 204 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here - 347 | long long y; - | ^ -In file included from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:27: -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:403:33: -/usr/include/c++/13/ostream:204:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] - 204 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here - 346 | long long extrapol; - | ^~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:404:26: -/usr/include/c++/13/ostream:204:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] - 204 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here - 347 | long long y; - | ^ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined 54 | #pragma GCC warning "WIN32 is NOT defined" | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp -[ 56%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:25: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp:25: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] @@ -1609,25 +1385,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = float; const_reference = const float&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] @@ -1638,6 +1395,16 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] 263 | if (index < 0 || index >= size()) | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 256 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = double; reference = double&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 263 | if (index < 0 || index >= size()) + | ~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = float]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:59:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] @@ -1648,6 +1415,11 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:73:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] 73 | Impl& operator=(void* cliNumericArray) | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:59:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 59 | Impl(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = float]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:287:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] @@ -1674,6 +1446,37 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:73:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 73 | Impl& operator=(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:287:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 287 | begin_ = iterator(binaryData, true); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:288:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 288 | end_ = iterator(binaryData, false); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:289:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 289 | cbegin_ = const_iterator(binaryData, true); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:290:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 290 | cend_ = const_iterator(binaryData, false); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = long int; const_reference = const long int&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:474:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] @@ -1684,13 +1487,13 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] 263 | if (index < 0 || index >= size()) | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = float; const_reference = const float&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] 256 | if (index < 0 || index >= size()) | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = double; reference = double&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = float; reference = float&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] 263 | if (index < 0 || index >= size()) | ~~~~~~^~~ @@ -1718,74 +1521,28 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:289:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 289 | cbegin_ = const_iterator(binaryData, true); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = float]': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:59:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] 59 | Impl(void* cliNumericArray) | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:290:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 290 | cend_ = const_iterator(binaryData, false); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:73:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 73 | Impl& operator=(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:472:30: required from here -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:287:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 287 | begin_ = iterator(binaryData, true); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:288:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 288 | end_ = iterator(binaryData, false); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:289:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:289:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] 289 | cbegin_ = const_iterator(binaryData, true); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:290:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:290:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] 290 | cend_ = const_iterator(binaryData, false); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = float; const_reference = const float&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 256 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = float; reference = float&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 263 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = float]': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:59:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 59 | Impl(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = float]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:73:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] 73 | Impl& operator=(void* cliNumericArray) | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = float]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:473:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:287:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] @@ -1812,25 +1569,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = long int; const_reference = const long int&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:474:30: required from here /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] @@ -1865,50 +1603,23 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:289:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] 289 | cbegin_ = const_iterator(binaryData, true); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.cpp:290:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] 290 | cend_ = const_iterator(binaryData, false); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Base64.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -1916,7 +1627,7 @@ from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Base64.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -1928,70 +1639,6 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:25: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Base64.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, @@ -2002,47 +1649,13 @@ | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Version.cpp -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2077,7 +1690,39 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:31: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Base64.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2112,11 +1757,9 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 26%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o +[ 27%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.cpp In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, @@ -2125,24 +1768,22 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:31: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, @@ -2151,71 +1792,162 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 30%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.cpp +[ 31%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp +[ 32%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp +[ 33%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o +[ 35%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp +[ 36%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 114 | } else if (init == mask) { + | ~~~~~^~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.cpp:25: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:30: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] + 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] + 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.cpp:25: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] + 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] + 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, + from /usr/include/boost/function/detail/prologue.hpp:12, + from /usr/include/boost/function.hpp:30, + from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, + from /usr/include/boost/algorithm/string/find_iterator.hpp:24, + from /usr/include/boost/algorithm/string/iter_find.hpp:27, + from /usr/include/boost/algorithm/string/split.hpp:16, + from /usr/include/boost/algorithm/string.hpp:23, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:34, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, + from /usr/include/boost/function/detail/prologue.hpp:12, + from /usr/include/boost/function.hpp:30, + from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, + from /usr/include/boost/algorithm/string/find_iterator.hpp:24, + from /usr/include/boost/algorithm/string/iter_find.hpp:27, + from /usr/include/boost/algorithm/string/split.hpp:16, + from /usr/include/boost/algorithm/string.hpp:23, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:34, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:27: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:403:33: +/usr/include/c++/13/ostream:204:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] + 204 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here + 346 | long long extrapol; + | ^~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:404:26: +/usr/include/c++/13/ostream:204:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] + 204 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here + 347 | long long y; + | ^ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 114 | } else if (init == mask) { + | ~~~~~^~~~~~~ +[ 38%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp +In file included from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:27: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:403:33: +/usr/include/c++/13/ostream:204:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] + 204 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here + 346 | long long extrapol; + | ^~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:404:26: +/usr/include/c++/13/ostream:204:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] + 204 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here + 347 | long long y; + | ^ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2235,63 +1967,66 @@ from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 60%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -[ 61%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumInfo.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:25: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:27, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:25: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2307,119 +2042,31 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:31: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:35: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:27, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2435,7 +2082,7 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2470,8 +2117,11 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.hpp:28: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, @@ -2488,56 +2138,92 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:286:24: warning: unused parameter 'filepath' [-Wunused-parameter] + 286 | const std::string& filepath, + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:287:10: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] + 287 | bool closeMemoryMappedSections) noexcept(true) { + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:556:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 556 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:575:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 575 | bfs::copy_directory(from, to, ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:618:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 618 | bfs::copy_directory(from, to, *ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:620:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 620 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:773:52: warning: unused parameter 'path' [-Wunused-parameter] + 773 | PWIZ_API_DECL void check_path_length(const string& path) { + | ~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:31: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 65%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:286:24: warning: unused parameter 'filepath' [-Wunused-parameter] + 286 | const std::string& filepath, + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:287:10: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] + 287 | bool closeMemoryMappedSections) noexcept(true) { + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:556:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 556 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:575:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 575 | bfs::copy_directory(from, to, ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:618:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 618 | bfs::copy_directory(from, to, *ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:620:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 620 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:773:52: warning: unused parameter 'path' [-Wunused-parameter] + 773 | PWIZ_API_DECL void check_path_length(const string& path) { + | ~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, @@ -2546,6 +2232,9 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 41%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp +[ 42%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:27, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:25: @@ -2564,27 +2253,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2605,7 +2280,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] 591 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] 593 | virtual Status endElement(const std::string& name, @@ -2620,15 +2294,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCV::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:81:47: warning: unused parameter 'position' [-Wunused-parameter] 81 | stream_offset position) @@ -2656,14 +2321,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:693:51: warning: unused parameter 'attributes' [-Wunused-parameter] 693 | const Attributes& attributes, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:694:47: warning: unused parameter 'position' [-Wunused-parameter] 694 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ @@ -2682,6 +2339,52 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1356:47: warning: unused parameter 'position' [-Wunused-parameter] 1356 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +[ 43%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 1657 | if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian) + | ^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 1660 | bool zlib = false; // Handle numpress+zlib + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] + 524 | bool useWorkerThreads) const + | ~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2169:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 2169 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrumListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2438:47: warning: unused parameter 'position' [-Wunused-parameter] + 2438 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerChromatogramListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2539:47: warning: unused parameter 'position' [-Wunused-parameter] + 2539 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2869:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 2869 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2787:47: warning: unused parameter 'position' [-Wunused-parameter] + 2787 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] + 524 | bool useWorkerThreads) const + | ~~~~~^~~~~~~~~~~~~~~~ +[ 45%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCV::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:81:47: warning: unused parameter 'position' [-Wunused-parameter] 81 | stream_offset position) @@ -2694,23 +2397,12 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:191:47: warning: unused parameter 'position' [-Wunused-parameter] 191 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 46%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerParamContainer::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:263:47: warning: unused parameter 'position' [-Wunused-parameter] 263 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 1657 | if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian) - | ^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 1660 | bool zlib = false; // Handle numpress+zlib - | ^~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerFileDescription::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:500:51: warning: unused parameter 'attributes' [-Wunused-parameter] 500 | const Attributes& attributes, @@ -2718,14 +2410,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:501:47: warning: unused parameter 'position' [-Wunused-parameter] 501 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerComponentList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:693:51: warning: unused parameter 'attributes' [-Wunused-parameter] 693 | const Attributes& attributes, @@ -2733,41 +2417,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:694:47: warning: unused parameter 'position' [-Wunused-parameter] 694 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerDataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:966:47: warning: unused parameter 'position' [-Wunused-parameter] 966 | stream_offset position) @@ -2783,18 +2432,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1356:47: warning: unused parameter 'position' [-Wunused-parameter] 1356 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2169:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 2169 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1657 | if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian) @@ -2802,24 +2439,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1660 | bool zlib = false; // Handle numpress+zlib | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrumListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2438:47: warning: unused parameter 'position' [-Wunused-parameter] - 2438 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerChromatogramListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2539:47: warning: unused parameter 'position' [-Wunused-parameter] - 2539 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2869:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 2869 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2787:47: warning: unused parameter 'position' [-Wunused-parameter] - 2787 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2169:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2169 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") @@ -2832,8 +2451,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2539:47: warning: unused parameter 'position' [-Wunused-parameter] 2539 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -[ 68%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2869:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2869 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || @@ -2841,65 +2458,343 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.cpp:2787:47: warning: unused parameter 'position' [-Wunused-parameter] 2787 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] - 524 | bool useWorkerThreads) const - | ~~~~~^~~~~~~~~~~~~~~~ +[ 47%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 48%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Version.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 50%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Version.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:27: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 51%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/XMLWriter.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] - 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] - 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, - from /usr/include/boost/function/detail/prologue.hpp:12, - from /usr/include/boost/function.hpp:30, - from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, - from /usr/include/boost/algorithm/string/find_iterator.hpp:24, - from /usr/include/boost/algorithm/string/iter_find.hpp:27, - from /usr/include/boost/algorithm/string/split.hpp:16, - from /usr/include/boost/algorithm/string.hpp:23, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:34, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:26: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2934,20 +2829,50 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:26: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] - 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] - 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, @@ -2956,55 +2881,20 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] - 524 | bool useWorkerThreads) const - | ~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp +[ 55%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp +[ 56%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] 121 | stream_offset position) @@ -3017,24 +2907,15 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] 356 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -[ 71%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] - 121 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] - 162 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] - 356 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] - 1112 | if ((result >= 0 && result < size()) || s == 0) - | ~~~~~~~^~~~ +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 57%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +[ 58%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp +[ 60%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:26: @@ -3053,21 +2934,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] - 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ +[ 61%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] + 121 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] + 162 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] + 356 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3083,14 +2966,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset '1' outside bounds of constant string [-Warray-bounds=] + 543 | Handler::Status status = wrangler.endElement(buffer.c_str()+1, position); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 62%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] + 549 | if (inCDATA) + | ^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here + 501 | bool inCDATA; + | ^~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:27: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -3108,16 +3004,9 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3133,25 +3022,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, - from /usr/include/boost/function/detail/prologue.hpp:12, - from /usr/include/boost/function.hpp:30, - from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, - from /usr/include/boost/algorithm/string/find_iterator.hpp:24, - from /usr/include/boost/algorithm/string/iter_find.hpp:27, - from /usr/include/boost/algorithm/string/split.hpp:16, - from /usr/include/boost/algorithm/string.hpp:23, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/String.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:34, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp:27: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3168,9 +3042,7 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3186,10 +3058,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:30: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3205,82 +3082,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp -[ 75%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] - 84 | } catch (index_not_found e){ - | ^ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] - 128 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] - 212 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] - 239 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] - 282 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] - 302 | virtual Status endElement(const std::string& name, stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 701 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] - 702 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] - 710 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] - 736 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] - 754 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 778 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] - 779 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] - 796 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] - 797 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] - 885 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 63%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.hpp:30: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': @@ -3292,25 +3100,24 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:35: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:29: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3321,8 +3128,7 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3338,21 +3144,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:583:9: note: here - 583 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] - 1115 | } - | ^ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] - 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSDataFile.cpp:35: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] @@ -3361,23 +3152,16 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } | ~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:24: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3397,15 +3181,6 @@ from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") @@ -3417,60 +3192,9 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 77%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp:27: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3486,11 +3210,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 1112 | if ((result >= 0 && result < size()) || s == 0) @@ -3503,18 +3229,40 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const | ~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const | ~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:32: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] + 1112 | if ((result >= 0 && result < size()) || s == 0) + | ~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] + 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3549,95 +3297,35 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:286:24: warning: unused parameter 'filepath' [-Wunused-parameter] - 286 | const std::string& filepath, - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:287:10: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] - 287 | bool closeMemoryMappedSections) noexcept(true) { - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:556:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 556 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:575:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 575 | bfs::copy_directory(from, to, ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:618:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 618 | bfs::copy_directory(from, to, *ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:620:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 620 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:773:52: warning: unused parameter 'path' [-Wunused-parameter] - 773 | PWIZ_API_DECL void check_path_length(const string& path) { - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] - 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -[ 81%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:26: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] + 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) + | ^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:583:9: note: here + 583 | case MS_Bruker_Agilent_YEP_nativeID_format: + | ^~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3672,52 +3360,109 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 205 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] - 206 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 82%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:28: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] + 1115 | } + | ^ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:82:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 82 | const Attributes& attributes, +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset '1' outside bounds of constant string [-Warray-bounds=] + 543 | Handler::Status status = wrangler.endElement(buffer.c_str()+1, position); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] + 549 | if (inCDATA) + | ^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here + 501 | bool inCDATA; + | ^~~~~~~ +[ 65%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] + 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) + | ^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:583:9: note: here + 583 | case MS_Bruker_Agilent_YEP_nativeID_format: + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] + 1115 | } + | ^ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] + 84 | } catch (index_not_found e){ + | ^ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] + 128 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] + 212 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] + 239 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] + 282 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] + 302 | virtual Status endElement(const std::string& name, stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 701 | const Attributes& attributes, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:83:47: warning: unused parameter 'position' [-Wunused-parameter] - 83 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] + 702 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:91:45: warning: unused parameter 'position' [-Wunused-parameter] - 91 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] + 710 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:116:47: warning: unused parameter 'position' [-Wunused-parameter] - 116 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] + 736 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:161:45: warning: unused parameter 'position' [-Wunused-parameter] - 161 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] + 754 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:197:47: warning: unused parameter 'position' [-Wunused-parameter] - 197 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 778 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] + 779 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] + 796 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] + 797 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] + 885 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] 84 | } catch (index_not_found e){ @@ -3779,35 +3524,77 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] 885 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:27: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_MGF.cpp:27: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:583:9: note: here - 583 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] - 1115 | } - | ^ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/LegacyAdapter.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 66%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp +[ 67%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 68%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp +[ 70%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 71%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 72%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] 302 | filterArray(byteBuffer, byteCount,compressed); @@ -3821,49 +3608,19 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here 132 | const void* byteBuffer; | ^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:286:24: warning: unused parameter 'filepath' [-Wunused-parameter] - 286 | const std::string& filepath, - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:287:10: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] - 287 | bool closeMemoryMappedSections) noexcept(true) { - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:556:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 556 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:575:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 575 | bfs::copy_directory(from, to, ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:618:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 618 | bfs::copy_directory(from, to, *ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:620:26: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 620 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.cpp:773:52: warning: unused parameter 'path' [-Wunused-parameter] - 773 | PWIZ_API_DECL void check_path_length(const string& path) { - | ~~~~~~~~~~~~~~^~~~ +[ 73%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp +[ 75%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3879,16 +3636,11 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 76%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:24: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3904,19 +3656,26 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3926,19 +3685,20 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 85%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp -[ 86%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:24: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:29: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3948,21 +3708,41 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 87%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp -[ 88%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] + 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3978,17 +3758,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 90%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp -[ 91%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 92%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, @@ -3996,7 +3765,7 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4031,45 +3800,63 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:29: +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:28: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:82:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 82 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:83:47: warning: unused parameter 'position' [-Wunused-parameter] + 83 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:91:45: warning: unused parameter 'position' [-Wunused-parameter] + 91 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:116:47: warning: unused parameter 'position' [-Wunused-parameter] + 116 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:161:45: warning: unused parameter 'position' [-Wunused-parameter] + 161 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:197:47: warning: unused parameter 'position' [-Wunused-parameter] + 197 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:31: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here + 131 | size_t byteCount; + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here + 132 | const void* byteBuffer; + | ^~~~~~~~~~ +[ 78%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:32: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -4108,32 +3895,100 @@ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp:25: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] + 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 205 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] + 206 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 80%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:24: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.hpp:31: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 93%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp -[ 95%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp -[ 96%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -[ 97%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp -cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: +[ 81%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:32: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4168,6 +4023,60 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 82%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 205 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] + 206 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 83%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp +[ 85%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -4203,31 +4112,6 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp:25: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/IO.hpp:32, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': @@ -4257,167 +4141,64 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Index_mzML.cpp:197:47: warning: unused parameter 'position' [-Wunused-parameter] 197 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:27: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:61:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 61 | sourceFile->id = sourceFile->name = BFS_STRING(p.leaf()); - | ~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:62:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 62 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); - | ~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 205 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] - 206 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::fillInCommonMetadata(const std::string&, pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:103:44: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 103 | msd.id = msd.run.id = bfs::basename(filename); - | ~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzML::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:122:68: warning: unused parameter 'filename' [-Wunused-parameter] - 122 | PWIZ_API_DECL std::string Reader_mzML::identify(const std::string& filename, const std::string& head) const - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:129:57: warning: unused parameter 'head' [-Wunused-parameter] - 129 | const std::string& head, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:132:52: warning: unused parameter 'config' [-Wunused-parameter] - 132 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzXML::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:197:69: warning: unused parameter 'filename' [-Wunused-parameter] - 197 | PWIZ_API_DECL std::string Reader_mzXML::identify(const std::string& filename, const std::string& head) const - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzXML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:212:58: warning: unused parameter 'head' [-Wunused-parameter] - 212 | const std::string& head, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:215:53: warning: unused parameter 'config' [-Wunused-parameter] - 215 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MGF::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:265:59: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 265 | return std::string(((bal::to_lower_copy(bfs::extension(filename)) == ".mgf"))?getType():""); - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:263:86: warning: unused parameter 'head' [-Wunused-parameter] - 263 | PWIZ_API_DECL std::string Reader_MGF::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:269:51: warning: unused parameter 'head' [-Wunused-parameter] - 269 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:272:51: warning: unused parameter 'config' [-Wunused-parameter] - 272 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:292:51: warning: unused parameter 'config' [-Wunused-parameter] - 292 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MSn::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:303:86: warning: unused parameter 'head' [-Wunused-parameter] - 303 | PWIZ_API_DECL std::string Reader_MSn::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:313:51: warning: unused parameter 'head' [-Wunused-parameter] - 313 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:316:51: warning: unused parameter 'config' [-Wunused-parameter] - 316 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:349:51: warning: unused parameter 'config' [-Wunused-parameter] - 349 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_BTDX::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:360:63: warning: unused parameter 'filename' [-Wunused-parameter] - 360 | PWIZ_API_DECL std::string Reader_BTDX::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:393:41: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 393 | sourceFile->name = BFS_STRING(p.leaf()); - | ~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:394:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 394 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); - | ~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:397:46: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 397 | result.id = result.run.id = bfs::basename(filename); - | ~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:376:52: warning: unused parameter 'head' [-Wunused-parameter] - 376 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:379:52: warning: unused parameter 'config' [-Wunused-parameter] - 379 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:406:52: warning: unused parameter 'config' [-Wunused-parameter] - 406 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mz5::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:425:62: warning: unused parameter 'filename' [-Wunused-parameter] - 425 | PWIZ_API_DECL std::string Reader_mz5::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:458:51: warning: unused parameter 'filename' [-Wunused-parameter] - 458 | PWIZ_API_DECL void Reader_mz5::read(const string& filename, - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:459:51: warning: unused parameter 'head' [-Wunused-parameter] - 459 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:460:45: warning: unused parameter 'result' [-Wunused-parameter] - 460 | MSData& result, - | ~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:461:41: warning: unused parameter 'runIndex' [-Wunused-parameter] - 461 | int runIndex, - | ~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:462:51: warning: unused parameter 'config' [-Wunused-parameter] - 462 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:484:51: warning: unused parameter 'config' [-Wunused-parameter] - 484 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ +[ 86%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/References.cpp:25: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 87%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp +[ 88%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: @@ -4436,11 +4217,182 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 90%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp +[ 91%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 92%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp +[ 93%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp +[ 95%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp:34: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.5/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.5/src -I/build/reproducible-path/libpwizlite-3.0.5/src/boost -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -c /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:28: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:30: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -4551,237 +4503,10 @@ /usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here 35 | inline std::string basename(const path& p) | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here - 131 | size_t byteCount; - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here - 132 | const void* byteBuffer; - | ^~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::vector pwiz::msdata::{anonymous}::getPrecursorInfo(const pwiz::msdata::Spectrum&, pwiz::msdata::SpectrumListPtr, pwiz::cv::CVID)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:421:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] 421 | const SpectrumListPtr spectrumListPtr, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'pwiz::cv::CVID pwiz::msdata::{anonymous}::translate_parentFilenameToSourceFileType(const std::string&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:832:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 832 | string fileExtension = bal::to_lower_copy(bfs::extension(name)); - | ~~~~~~~~~~~~~~^~~~~~ -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerScanFileContent::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:976:47: warning: unused parameter 'position' [-Wunused-parameter] - 976 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'void pwiz::msdata::{anonymous}::fillInMetadata(pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1088:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 1088 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).leaf()); - | ~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1090:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 1090 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).parent_path().leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1105:47: warning: unused parameter 'position' [-Wunused-parameter] - 1105 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1186:45: warning: unused parameter 'position' [-Wunused-parameter] - 1186 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_dataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1234:47: warning: unused parameter 'position' [-Wunused-parameter] - 1234 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_mzXML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1302:47: warning: unused parameter 'position' [-Wunused-parameter] - 1302 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:27: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] - 40 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] - 88 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] - 124 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp:25067: -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] - 102 | for (int o=0;o instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:27: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] - 40 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] - 88 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] - 124 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:28: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -4824,6 +4549,13 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'pwiz::cv::CVID pwiz::msdata::{anonymous}::translate_parentFilenameToSourceFileType(const std::string&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:832:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 832 | string fileExtension = bal::to_lower_copy(bfs::extension(name)); + | ~~~~~~~~~~~~~~^~~~~~ +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Reader.hpp:29: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] @@ -4849,17 +4581,68 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerScanFileContent::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:976:47: warning: unused parameter 'position' [-Wunused-parameter] + 976 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'void pwiz::msdata::{anonymous}::fillInMetadata(pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1088:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 1088 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).leaf()); + | ~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1090:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 1090 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).parent_path().leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1105:47: warning: unused parameter 'position' [-Wunused-parameter] + 1105 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1186:45: warning: unused parameter 'position' [-Wunused-parameter] + 1186 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_dataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1234:47: warning: unused parameter 'position' [-Wunused-parameter] + 1234 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_mzXML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:1302:47: warning: unused parameter 'position' [-Wunused-parameter] + 1302 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Exception.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:28: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4869,41 +4652,159 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:27: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:61:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 61 | sourceFile->id = sourceFile->name = BFS_STRING(p.leaf()); + | ~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:62:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 62 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); + | ~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::fillInCommonMetadata(const std::string&, pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:103:44: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 103 | msd.id = msd.run.id = bfs::basename(filename); + | ~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:37: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzML::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:122:68: warning: unused parameter 'filename' [-Wunused-parameter] + 122 | PWIZ_API_DECL std::string Reader_mzML::identify(const std::string& filename, const std::string& head) const + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:129:57: warning: unused parameter 'head' [-Wunused-parameter] + 129 | const std::string& head, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:132:52: warning: unused parameter 'config' [-Wunused-parameter] + 132 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzXML::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:197:69: warning: unused parameter 'filename' [-Wunused-parameter] + 197 | PWIZ_API_DECL std::string Reader_mzXML::identify(const std::string& filename, const std::string& head) const + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzXML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:212:58: warning: unused parameter 'head' [-Wunused-parameter] + 212 | const std::string& head, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:215:53: warning: unused parameter 'config' [-Wunused-parameter] + 215 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MGF::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:265:59: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 265 | return std::string(((bal::to_lower_copy(bfs::extension(filename)) == ".mgf"))?getType():""); + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:263:86: warning: unused parameter 'head' [-Wunused-parameter] + 263 | PWIZ_API_DECL std::string Reader_MGF::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:269:51: warning: unused parameter 'head' [-Wunused-parameter] + 269 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:272:51: warning: unused parameter 'config' [-Wunused-parameter] + 272 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:292:51: warning: unused parameter 'config' [-Wunused-parameter] + 292 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MSn::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:303:86: warning: unused parameter 'head' [-Wunused-parameter] + 303 | PWIZ_API_DECL std::string Reader_MSn::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:313:51: warning: unused parameter 'head' [-Wunused-parameter] + 313 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:316:51: warning: unused parameter 'config' [-Wunused-parameter] + 316 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:349:51: warning: unused parameter 'config' [-Wunused-parameter] + 349 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_BTDX::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:360:63: warning: unused parameter 'filename' [-Wunused-parameter] + 360 | PWIZ_API_DECL std::string Reader_BTDX::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:393:41: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 393 | sourceFile->name = BFS_STRING(p.leaf()); + | ~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:394:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 394 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); + | ~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:397:46: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 397 | result.id = result.run.id = bfs::basename(filename); + | ~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:376:52: warning: unused parameter 'head' [-Wunused-parameter] + 376 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:379:52: warning: unused parameter 'config' [-Wunused-parameter] + 379 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:406:52: warning: unused parameter 'config' [-Wunused-parameter] + 406 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mz5::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:425:62: warning: unused parameter 'filename' [-Wunused-parameter] + 425 | PWIZ_API_DECL std::string Reader_mz5::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:458:51: warning: unused parameter 'filename' [-Wunused-parameter] + 458 | PWIZ_API_DECL void Reader_mz5::read(const string& filename, + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:459:51: warning: unused parameter 'head' [-Wunused-parameter] + 459 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:460:45: warning: unused parameter 'result' [-Wunused-parameter] + 460 | MSData& result, + | ~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:461:41: warning: unused parameter 'runIndex' [-Wunused-parameter] + 461 | int runIndex, + | ~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:462:51: warning: unused parameter 'config' [-Wunused-parameter] + 462 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:484:51: warning: unused parameter 'config' [-Wunused-parameter] + 484 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp:34: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:27: /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:61:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] @@ -4935,6 +4836,13 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:122:68: warning: unused parameter 'filename' [-Wunused-parameter] 122 | PWIZ_API_DECL std::string Reader_mzML::identify(const std::string& filename, const std::string& head) const | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:129:57: warning: unused parameter 'head' [-Wunused-parameter] 129 | const std::string& head, @@ -5049,6 +4957,154 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/DefaultReaderList.cpp:484:51: warning: unused parameter 'config' [-Wunused-parameter] 484 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:27: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/ParamTypes.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:27: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] + 40 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] + 88 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] + 124 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp:34: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.cpp:25067: +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': +/build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 102 | for (int o=0;o instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::string pwiz::msdata::{anonymous}::translate_SourceFileTypeToRunID(const pwiz::msdata::SourceFile&, pwiz::cv::CVID)': /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/msdata/Serializer_mzXML.cpp:128:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 128 | string nameExtension = bal::to_lower_copy(bfs::extension(sf.name)); @@ -5211,36 +5267,16 @@ /build/reproducible-path/libpwizlite-3.0.5/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 102 | for (int o=0;o