Diff of the two buildlogs: -- --- b1/build.log 2023-04-22 06:46:19.855394716 +0000 +++ b2/build.log 2023-04-22 06:49:21.983319910 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 24 01:07:36 -12 2024 -I: pbuilder-time-stamp: 1716556056 +I: Current time: Sat Apr 22 20:46:23 +14 2023 +I: pbuilder-time-stamp: 1682145983 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 15 19:23:47 2022 -12 +gpgv: Signature made Sun Jan 16 21:23:47 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,52 +28,84 @@ dpkg-source: info: applying fix_example.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24395/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-arm64. +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 Apr 22 20:46 /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/26362/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='24395' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=26362 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.R9BQoR2V/pbuilderrc_aTfR --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.R9BQoR2V/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.R9BQoR2V/pbuilderrc_8uGW --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.R9BQoR2V/b2 --logfile b2/build.log --extrapackages usrmerge baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 21 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/24395/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -148,7 +180,7 @@ Get: 31 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 help2man arm64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] -Fetched 21.9 MB in 2s (10.5 MB/s) +Fetched 21.9 MB in 1s (36.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19616 files and directories currently installed.) @@ -294,8 +326,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -338,8 +379,8 @@ CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ -In file included from CSequences2.h:42, - from bait-fisher-helper.cpp:32: +In file included from CSeqNameList.h:38, + from CBlastParser.h:52: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; @@ -414,16 +455,21 @@ CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ -In file included from CSeqNameList.h:38, - from CBlastParser.h:52: -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': -CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 283 | register char c; - | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ +In file included from CSequence_Mol2_1.h:50, + from GFF-class.h:34, + from bait-fisher.cpp:30: +CFile/CFile2_1.h: In member function 'char CFile::getchar()': +CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 256 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': +CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 283 | register char c; + | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; @@ -455,6 +501,12 @@ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ +In file included from CSequences2.h:42, + from bait-fisher-helper.cpp:32: +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': +CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 283 | register char c; + | ^ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ @@ -464,6 +516,34 @@ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': +CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 300 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': +CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 321 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': +CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 340 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': +CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 342 | register char local_general_ambig = toupper(general_ambig); + | ^~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2627 | register bool removegaps_bool = (pflag & removegaps); // + | ^~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2628 | register bool removestars_bool = (pflag & removestars); // + | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; @@ -483,73 +563,6 @@ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': -CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 685 | register char c; - | ^ -CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 687 | register char local_general_ambig = toupper(general_ambig); - | ^~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': -CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 764 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': -CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 825 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': -CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2627 | register bool removegaps_bool = (pflag & removegaps); // - | ^~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2628 | register bool removestars_bool = (pflag & removestars); // - | ^~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': -CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2627 | register bool removegaps_bool = (pflag & removegaps); // - | ^~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2628 | register bool removestars_bool = (pflag & removestars); // - | ^~~~~~~~~~~~~~~~ -In file included from CSequence_Mol2_1.h:50, - from GFF-class.h:34, - from bait-fisher.cpp:30: -CFile/CFile2_1.h: In member function 'char CFile::getchar()': -CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 256 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': -CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 283 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': -CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 300 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': -CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 321 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': -CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 340 | register char c; - | ^ -CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 342 | register char local_general_ambig = toupper(general_ambig); - | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; @@ -560,6 +573,13 @@ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': +CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 685 | register char c; + | ^ +CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 687 | register char local_general_ambig = toupper(general_ambig); + | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ @@ -575,6 +595,22 @@ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ +In file included from CSequence_Mol2_1.h:50, + from CSequences2.h:42, + from Csequence_cluster_and_center_sequence.h:44, + from Csequence_cluster_and_center_sequence.cpp:27: +CFile/CFile2_1.h: In member function 'char CFile::getchar()': +CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 256 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': +CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 764 | register char c; + | ^ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': +CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 825 | register char c; + | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; @@ -609,31 +645,10 @@ CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ -In file included from CSequence_Mol2_1.h:50, - from CSequences2.h:42, - from Csequence_cluster_and_center_sequence.h:44, - from Csequence_cluster_and_center_sequence.cpp:27: -CFile/CFile2_1.h: In member function 'char CFile::getchar()': -CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 256 | register char c; - | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': -CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // - | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ -CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2627 | register bool removegaps_bool = (pflag & removegaps); // - | ^~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2628 | register bool removestars_bool = (pflag & removestars); // - | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; @@ -721,6 +736,32 @@ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': +CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2627 | register bool removegaps_bool = (pflag & removegaps); // + | ^~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2628 | register bool removestars_bool = (pflag & removestars); // + | ^~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': +CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2627 | register bool removegaps_bool = (pflag & removegaps); // + | ^~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2628 | register bool removestars_bool = (pflag & removestars); // + | ^~~~~~~~~~~~~~~~ g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-filter.o global-types-and-parameters.o -o BaitFilter-v1.0.6 g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-fisher-helper.o bait-fisher.o Csequence_cluster_and_center_sequence.o mydir-unix.o -o BaitFisher-v1.2.8 make[1]: Leaving directory '/build/baitfisher-1.2.7+git20211020.de26d5c+dfsg' @@ -762,8 +803,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_arm64.deb'. dpkg-deb: building package 'baitfisher' in '../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_arm64.deb'. +dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -771,12 +812,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/26362/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26362/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/24395 and its subdirectories -I: Current time: Fri May 24 01:09:17 -12 2024 -I: pbuilder-time-stamp: 1716556157 +I: removing directory /srv/workspace/pbuilder/26362 and its subdirectories +I: Current time: Sat Apr 22 20:49:20 +14 2023 +I: pbuilder-time-stamp: 1682146160