Diff of the two buildlogs: -- --- b1/build.log 2024-05-31 14:52:51.383521901 +0000 +++ b2/build.log 2024-05-31 15:05:20.719644735 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 3 09:13:05 -12 2025 -I: pbuilder-time-stamp: 1751577185 +I: Current time: Sat Jun 1 04:52:54 +14 2024 +I: pbuilder-time-stamp: 1717167174 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying fix-system.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2959796/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 31 14:53 /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/3739232/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3739232/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4e4ac888177c4e4b85c0a27be2f5cce9' - 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='2959796' - PS1='# ' - PS2='> ' + INVOCATION_ID=2359c0e0d87b4c08b6b4177012f7d4a3 + 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=3739232 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.DfU5W34l/pbuilderrc_kEmP --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DfU5W34l/b1 --logfile b1/build.log libmems_1.6.0+4725-10.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.DfU5W34l/pbuilderrc_44Db --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DfU5W34l/b2 --logfile b2/build.log libmems_1.6.0+4725-10.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2959796/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -186,7 +218,7 @@ Get: 53 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 44.3 MB in 4s (11.7 MB/s) +Fetched 44.3 MB in 3s (17.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19719 files and directories currently installed.) @@ -421,7 +453,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libmems-1.6.0+4725/ && 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 > ../libmems_1.6.0+4725-10_source.changes +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libmems-1.6.0+4725/ && 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 > ../libmems_1.6.0+4725-10_source.changes dpkg-buildpackage: info: source package libmems dpkg-buildpackage: info: source version 1.6.0+4725-10 dpkg-buildpackage: info: source distribution unstable @@ -664,259 +700,57 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j42 + make -j20 make[1]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' make all-recursive make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' Making all in libMems make[3]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o RepeatHash.lo RepeatHash.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o DNAFileSML.lo DNAFileSML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o MatchFinder.lo MatchFinder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o DNAMemorySML.lo DNAMemorySML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o MemorySML.lo MemorySML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o SortedMerList.lo SortedMerList.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 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MatchHashEntry.lo MatchHashEntry.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Interval.lo Interval.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o IntervalList.lo IntervalList.cpp -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 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-Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o MuscleInterface.lo MuscleInterface.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o PhyloTree.lo PhyloTree.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 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-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c twister.c -fPIC -DPIC -o .libs/twister.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/util.c -fPIC -DPIC -o .libs/util.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o -dmSML/util.c: In function 'removeFile': -dmSML/util.c:127:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 127 | rm_cmd = Fmt( "/bin/rm -fv %s", filename ); - | ^ -dmSML/util.c:129:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 129 | rm_cmd = Fmt( "/bin/rm -f %s", filename ); - | ^ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 -dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO': -dmSML/aPOSIXaio.c:115:28: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types] - 115 | rval = aio_suspend(request_array, 1, &zero_wait); - | ^~~~~~~~~~~~~ - | | - | struct aiocb ** -In file included from /usr/include/features.h:502, - from /usr/include/x86_64-linux-gnu/sys/types.h:25, - from ../libMems/dmSML/asyncio.h:24, - from ../libMems/dmSML/aPOSIXaio.h:8, - from dmSML/aPOSIXaio.c:5: -/usr/include/aio.h:202:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' - 202 | extern int __REDIRECT_NTH (aio_suspend, - | ^~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/ext/hash_map:60, - from HomologyHMM/dptables.h:43, - from HomologyHMM/homology.h:27, - from HomologyHMM/homology.cc:24: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 -In file included from /usr/include/c++/13/ext/hash_map:60, - from HomologyHMM/dptables.h:43, - from HomologyHMM/homology.h:27, - from HomologyHMM/homologymain.cc:21: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/timing.c -o timing.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/util.c -o util.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sml.c -o sml.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c twister.c -o twister.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 -In file included from HomologyHMM/algebras.cc:27: -HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 190 | register BFloat a( 0.0, 0 ); - | ^ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 209 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 236 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 -In file included from HomologyHMM/homology.h:28: -HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 190 | register BFloat a( 0.0, 0 ); - | ^ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 209 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 236 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ -In file included from HomologyHMM/homology.h:28: -HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 190 | register BFloat a( 0.0, 0 ); - | ^ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 209 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 236 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ -In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from Islands.cpp:13: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from ../libMems/ProgressiveAligner.h:21, - from ProgressiveAligner.cpp:14: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -HomologyHMM/homology.cc: In function 'Algebra Forward(HomologyDPTable**, Params, char*, int)': -HomologyHMM/homology.cc:319:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 319 | register double iTempResult[1]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 321 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Algebra Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)': -HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 417 | register double iTempResult[1]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 419 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Algebra Viterbi_recurse(HomologyDPTable**, Params, char*, int)': -HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 565 | register double iTempResult[1]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 567 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)': -HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 673 | register double iTempResult[1]; - | ^~~~~~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o RepeatMatchList.lo RepeatMatchList.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 -In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from ../libMems/ProgressiveAligner.h:21, - from Backbone.cpp:13: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 In file included from /usr/include/c++/13/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, @@ -929,18 +763,21 @@ from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, - from ../libMems/ProgressiveAligner.h:21, - from GreedyBreakpointElimination.cpp:7: + from Islands.cpp:13: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o RepeatMatch.lo RepeatMatch.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Backbone.lo Backbone.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, - from MemHash.cpp:13: + from ../libMems/RepeatHash.h:16, + from RepeatHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -979,8 +816,8 @@ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, - from ../libMems/RepeatHash.h:16, - from RepeatHash.cpp:13: + from ../libMems/IntervalList.h:23, + from IntervalList.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -998,7 +835,9 @@ | ^~~~ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, - from MatchFinder.cpp:13: + from ../libMems/MemHash.h:20, + from ../libMems/MaskedMemHash.h:16, + from MaskedMemHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1014,11 +853,11 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, - from ../libMems/IntervalList.h:23, - from IntervalList.cpp:13: + from MemHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1034,30 +873,9 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -In file included from ../libMems/HomologyHMM/homology.h:28: -../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 190 | register BFloat a( 0.0, 0 ); - | ^ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 209 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 236 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, - from Aligner.cpp:9: + from FileSML.cpp:12: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1074,10 +892,8 @@ 1127 | path leaf() const { return filename(); } | ^~~~ In file included from ../libMems/MatchList.h:25, - from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from ../libMems/MaskedMemHash.h:16, - from MaskedMemHash.cpp:13: + from ../libMems/Aligner.h:19, + from Aligner.cpp:9: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1093,10 +909,9 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, - from ../libMems/Aligner.h:19, - from ../libMems/ProgressiveAligner.h:17: + from ../libMems/MatchFinder.h:18, + from MatchFinder.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1113,10 +928,7 @@ 1127 | path leaf() const { return filename(); } | ^~~~ In file included from ../libMems/MatchList.h:25, - from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from ../libMems/PairwiseMatchFinder.h:16, - from PairwiseMatchFinder.cpp:13: + from MatchList.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1132,6 +944,36 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from ../libMems/ProgressiveAligner.h:21, + from Backbone.cpp:13: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +In file included from ../libMems/HomologyHMM/homology.h:28: +../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 190 | register BFloat a( 0.0, 0 ); + | ^ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 209 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 236 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ In file included from ../libMems/MatchList.h:25, from ../libMems/RepeatMatchList.h:21, from RepeatMatchList.cpp:13: @@ -1150,8 +992,53 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +In file included from ../libMems/HomologyHMM/homology.h:28: +../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 190 | register BFloat a( 0.0, 0 ); + | ^ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 209 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 236 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ProgressiveAligner.lo ProgressiveAligner.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o SuperInterval.lo SuperInterval.cpp +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from ../libMems/ProgressiveAligner.h:21, + from ProgressiveAligner.cpp:14: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Interval.cpp -o Interval.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, - from MatchList.cpp:13: + from ../libMems/Aligner.h:19, + from ../libMems/ProgressiveAligner.h:17: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1167,6 +1054,9 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1188,15 +1078,17 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -In file included from ../libMems/SeedOccurrenceList.h:9, - from ../libMems/GreedyBreakpointElimination.h:13, - from GreedyBreakpointElimination.cpp:6: +In file included from ../libMems/MatchList.h:25, + from ../libMems/MatchFinder.h:18, + from ../libMems/MemHash.h:20, + from ../libMems/PairwiseMatchFinder.h:16, + from PairwiseMatchFinder.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem.hpp:16, - from ../libMems/SeedOccurrenceList.h:7: +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from ../libMems/Files.h:23: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ @@ -1206,9 +1098,69 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o +In file included from /usr/include/c++/13/ext/hash_map:60, + from HomologyHMM/dptables.h:43, + from HomologyHMM/homology.h:27, + from HomologyHMM/homology.cc:24: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +In file included from HomologyHMM/homology.h:28: +HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 190 | register BFloat a( 0.0, 0 ); + | ^ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 209 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 236 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ +HomologyHMM/homology.cc: In function 'Algebra Forward(HomologyDPTable**, Params, char*, int)': +HomologyHMM/homology.cc:319:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 319 | register double iTempResult[1]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 321 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Algebra Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)': +HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 417 | register double iTempResult[1]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 419 | register bfloat iTempProb[3]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Algebra Viterbi_recurse(HomologyDPTable**, Params, char*, int)': +HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 565 | register double iTempResult[1]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 567 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)': +HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 673 | register double iTempResult[1]; + | ^~~~~~~~~~~ In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, - from FileSML.cpp:12: + from ../libMems/ProgressiveAligner.h:17: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -1224,6 +1176,38 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +In file included from HomologyHMM/algebras.cc:27: +HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 190 | register BFloat a( 0.0, 0 ); + | ^ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 209 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 236 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from ../libMems/ProgressiveAligner.h:21, + from GreedyBreakpointElimination.cpp:7: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1245,15 +1229,25 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -In file included from ../libMems/MatchList.h:25, - from ../libMems/Aligner.h:19, - from ../libMems/ProgressiveAligner.h:17: +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o +In file included from /usr/include/c++/13/ext/hash_map:60, + from HomologyHMM/dptables.h:43, + from HomologyHMM/homology.h:27, + from HomologyHMM/homologymain.cc:21: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 +In file included from ../libMems/SeedOccurrenceList.h:9, + from ../libMems/GreedyBreakpointElimination.h:13, + from GreedyBreakpointElimination.cpp:6: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from ../libMems/Files.h:23: +In file included from /usr/include/boost/filesystem.hpp:16, + from ../libMems/SeedOccurrenceList.h:7: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ @@ -1263,31 +1257,39 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Interval.cpp -o Interval.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 -In file included from ../libMems/HomologyHMM/homology.h:28: -../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 +In file included from HomologyHMM/homology.h:28: +HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 190 | register BFloat a( 0.0, 0 ); | ^ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 209 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 216 | register double mantisse = a.f*b; | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 229 | register double mantisse = a.f*b; | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1309,24 +1311,58 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o +dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO': +dmSML/aPOSIXaio.c:115:28: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types] + 115 | rval = aio_suspend(request_array, 1, &zero_wait); + | ^~~~~~~~~~~~~ + | | + | struct aiocb ** +In file included from /usr/include/features.h:502, + from /usr/include/x86_64-linux-gnu/sys/types.h:25, + from ../libMems/dmSML/asyncio.h:24, + from ../libMems/dmSML/aPOSIXaio.h:8, + from dmSML/aPOSIXaio.c:5: +/usr/include/aio.h:202:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' + 202 | extern int __REDIRECT_NTH (aio_suspend, + | ^~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/util.c -fPIC -DPIC -o .libs/util.o +dmSML/util.c: In function 'removeFile': +dmSML/util.c:127:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 127 | rm_cmd = Fmt( "/bin/rm -fv %s", filename ); + | ^ +dmSML/util.c:129:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 129 | rm_cmd = Fmt( "/bin/rm -f %s", filename ); + | ^ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/util.c -o util.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/timing.c -o timing.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/sml.c -o sml.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Islands.cpp -o Islands.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/x86_64-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread +/bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/x86_64-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems.so.1 -o .libs/libMems.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libMems.so.1" && ln -s "libMems.so.1.0.0" "libMems.so.1") libtool: link: (cd ".libs" && rm -f "libMems.so" && ln -s "libMems.so.1.0.0" "libMems.so") @@ -1339,7 +1375,7 @@ make[2]: Leaving directory '/build/reproducible-path/libmems-1.6.0+4725' make[1]: Leaving directory '/build/reproducible-path/libmems-1.6.0+4725' dh_auto_test - make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 + make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' Making check in libMems make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' @@ -1357,7 +1393,7 @@ make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' /usr/bin/mkdir -p '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems.so.1.0.0 libtool: install: (cd /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so.1 || { rm -f libMems.so.1 && ln -s libMems.so.1.0.0 libMems.so.1; }; }) libtool: install: (cd /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; }) @@ -1443,12 +1479,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3739232/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2959796 and its subdirectories -I: Current time: Thu Jul 3 09:15:50 -12 2025 -I: pbuilder-time-stamp: 1751577350 +I: removing directory /srv/workspace/pbuilder/3739232 and its subdirectories +I: Current time: Sat Jun 1 05:05:19 +14 2024 +I: pbuilder-time-stamp: 1717167919