Diff of the two buildlogs: -- --- b1/build.log 2025-03-19 18:56:32.594672475 +0000 +++ b2/build.log 2025-03-19 18:58:02.002637996 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 21 13:18:40 -12 2026 -I: pbuilder-time-stamp: 1776820720 +I: Current time: Thu Mar 20 08:56:34 +14 2025 +I: pbuilder-time-stamp: 1742410594 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,54 +30,86 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/38136/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5180/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Mar 19 18:56 /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/5180/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5180/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f68d57b4257b48c8b5236f42b7d4067e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='38136' - PS1='# ' - PS2='> ' + INVOCATION_ID=3467c6109e794ad38b286996c706a9bb + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=5180 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.67SBByhQ/pbuilderrc_orcr --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.67SBByhQ/b1 --logfile b1/build.log pirs_2.0.2+dfsg-12.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.67SBByhQ/pbuilderrc_hzbb --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.67SBByhQ/b2 --logfile b2/build.log pirs_2.0.2+dfsg-12.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos16-i386 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/38136/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/5180/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -154,7 +186,7 @@ Get: 33 http://deb.debian.org/debian unstable/main i386 libgzstream0 i386 1.5+git20171107.9a20658-3 [7192 B] Get: 34 http://deb.debian.org/debian unstable/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-3 [7568 B] Get: 35 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 32.7 MB in 0s (134 MB/s) +Fetched 32.7 MB in 0s (72.3 MB/s) Preconfiguring packages ... 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 ... 19770 files and directories currently installed.) @@ -309,7 +341,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pirs-2.0.2+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 > ../pirs_2.0.2+dfsg-12_source.changes +I: user script /srv/workspace/pbuilder/5180/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/5180/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pirs-2.0.2+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 > ../pirs_2.0.2+dfsg-12_source.changes dpkg-buildpackage: info: source package pirs dpkg-buildpackage: info: source version 2.0.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable @@ -404,7 +440,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg' dh_auto_build - cd src && make -j22 + cd src && make -j10 make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' make all-recursive make[3]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' @@ -420,14 +456,13 @@ g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp pirs_diploid.cpp:640:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ @@ -449,138 +484,6 @@ pirs_diploid.cpp:644:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 644 | info(" %#"PRIx64"]\n", het_type_tab[6]); | ^ -pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 168 | " "DEFAULT_BASE_CALLING_PROFILE"\n" - | ^ -pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 174 | " "DEFAULT_INDEL_PROFILE"\n" - | ^ -pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 180 | " "DEFAULT_GC_BIAS_PROFILE_100",\n" - | ^ -pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 181 | " "DEFAULT_GC_BIAS_PROFILE_150",\n" - | ^ -pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n" - | ^ -pirs_simulate.cpp:672:25: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n", - | ^ -pirs_simulate.cpp:700:30: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 700 | info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t", - | ^ -pirs_simulate.cpp:1235:38: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", - | ^ -pirs_simulate.cpp:1235:57: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", - | ^ -pirs_simulate.cpp:1540:35: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second); - | ^ -pirs_simulate.cpp:1557:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1557 | "# The total number of read pairs that were simulated was %"PRIu64".\n" - | ^ -pirs_simulate.cpp:1574:34: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1574 | error_log.printf("%d\t%"PRIu64"\t%g\n", - | ^ -pirs_simulate.cpp:1579:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1579 | error_log.printf("total\t%"PRIu64"\t%g\n", - | ^ -pirs_simulate.cpp:1685:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1685 | log_parameter(info_log, "Random seed: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1713:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1713 | info("Program: "PROGRAM "\n"); - | ^ -pirs_simulate.cpp:1714:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1714 | info("Version: "VERSION "\n"); - | ^ -pirs_simulate.cpp:1715:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1715 | info("Author: "AUTHOR "\n"); - | ^ -pirs_simulate.cpp:1716:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1716 | info("Contact: "CONTACT "\n"); - | ^ -pirs_simulate.cpp:1717:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^ -pirs_simulate.cpp:1717:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^~~~~~~~ -pirs_simulate.cpp:1717:51: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^~~~~~~~ -pirs_simulate.cpp:1764:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1764 | info("Bases in reference sequences: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1766:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1766 | info("Read pairs simulated: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1768:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1768 | info("Bases in reads: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1773:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1773 | info("Substitution error count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1777:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1777 | info("Insertion count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1779:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1779 | info("Deletion count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1795:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases); - | ^ -pirs_simulate.cpp:1856:22: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1856 | info("Note: A random seed (%"PRIu64") was specified on the command line.\n", - | ^ -In file included from OutputStream.cpp:1: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -In file included from InputStream.cpp:1: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -InputStream.h: In constructor 'InputStream::InputStream(const char*)': -InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -In file included from Profile.cpp:2: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -InputStream.h: In constructor 'InputStream::InputStream(const char*)': -InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ In file included from util.cpp:18: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] @@ -612,9 +515,39 @@ | | size_t {aka unsigned int} | long unsigned int | %u +In file included from OutputStream.cpp:1: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +In file included from InputStream.cpp:1: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +InputStream.h: In constructor 'InputStream::InputStream(const char*)': +InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp In file included from SimulationParameters.h:6, - from GCBiasProfile.h:5, - from GCBiasProfile.cpp:5: + from IndelProfile.cpp:2: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -644,9 +577,37 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -In file included from SimulationParameters.h:6, - from BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: +IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)': +IndelProfile.cpp:117:51: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] + 117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1) + | ~~^ ~~ + | | | + | | uint64_t* {aka long long unsigned int*} + | long unsigned int* + | %llu +IndelProfile.cpp:119:49: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] + 119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1) + | ~~^ ~~ + | | | + | | uint64_t* {aka long long unsigned int*} + | long unsigned int* + | %llu +IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)': +IndelProfile.cpp:165:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 165 | info(" read_1_count = %lu\n", read_1_count); + | ~~^ ~~~~~~~~~~~~ + | | | + | | uint64_t {aka long long unsigned int} + | long unsigned int + | %llu +IndelProfile.cpp:166:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 166 | info(" read_2_count = %lu\n", read_2_count); + | ~~^ ~~~~~~~~~~~~ + | | | + | | uint64_t {aka long long unsigned int} + | long unsigned int + | %llu +In file included from Profile.cpp:2: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -661,7 +622,22 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -In file included from SimulationParameters.h:7: +In file included from pirs_diploid.cpp:12: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +InputStream.h: In constructor 'InputStream::InputStream(const char*)': +InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +In file included from pirs_diploid.cpp:13: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 54 | memset(this, 0, sizeof(*this)); @@ -676,8 +652,30 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ +pirs_diploid.cpp: In function 'bool try_indel(const double*, const size_t*, const std::vector&, size_t&, std::vector&, bool, const char*, Counter&)': +pirs_diploid.cpp:436:46: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", + | ~~^ + | | + | unsigned int + | %llu + 437 | id, log_ref_seq_idx, log_diploid_seq_idx, + | ~~~~~~~~~~~~~~~ + | | + | uint64_t {aka long long unsigned int} +pirs_diploid.cpp:436:51: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", + | ~~^ + | | + | unsigned int + | %llu + 437 | id, log_ref_seq_idx, log_diploid_seq_idx, + | ~~~~~~~~~~~~~~~~~~~ + | | + | uint64_t {aka long long unsigned int} In file included from SimulationParameters.h:6, - from IndelProfile.cpp:2: + from GCBiasProfile.h:5, + from GCBiasProfile.cpp:5: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -707,7 +705,9 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -In file included from pirs_diploid.cpp:12: +In file included from SimulationParameters.h:6, + from BaseCallingProfile.h:7, + from BaseCallingProfile.cpp:5: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -722,7 +722,7 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -In file included from pirs_diploid.cpp:13: +In file included from SimulationParameters.h:7: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 54 | memset(this, 0, sizeof(*this)); @@ -737,57 +737,93 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -pirs_diploid.cpp: In function 'bool try_indel(const double*, const size_t*, const std::vector&, size_t&, std::vector&, bool, const char*, Counter&)': -pirs_diploid.cpp:436:46: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", - | ~~^ - | | - | unsigned int - | %llu - 437 | id, log_ref_seq_idx, log_diploid_seq_idx, - | ~~~~~~~~~~~~~~~ - | | - | uint64_t {aka long long unsigned int} -pirs_diploid.cpp:436:51: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", - | ~~^ - | | - | unsigned int - | %llu - 437 | id, log_ref_seq_idx, log_diploid_seq_idx, - | ~~~~~~~~~~~~~~~~~~~ - | | - | uint64_t {aka long long unsigned int} -IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)': -IndelProfile.cpp:117:51: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] - 117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1) - | ~~^ ~~ - | | | - | | uint64_t* {aka long long unsigned int*} - | long unsigned int* - | %llu -IndelProfile.cpp:119:49: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] - 119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1) - | ~~^ ~~ - | | | - | | uint64_t* {aka long long unsigned int*} - | long unsigned int* - | %llu -IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)': -IndelProfile.cpp:165:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 165 | info(" read_1_count = %lu\n", read_1_count); - | ~~^ ~~~~~~~~~~~~ - | | | - | | uint64_t {aka long long unsigned int} - | long unsigned int - | %llu -IndelProfile.cpp:166:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 166 | info(" read_2_count = %lu\n", read_2_count); - | ~~^ ~~~~~~~~~~~~ - | | | - | | uint64_t {aka long long unsigned int} - | long unsigned int - | %llu +pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 168 | " "DEFAULT_BASE_CALLING_PROFILE"\n" + | ^ +pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 174 | " "DEFAULT_INDEL_PROFILE"\n" + | ^ +pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 180 | " "DEFAULT_GC_BIAS_PROFILE_100",\n" + | ^ +pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 181 | " "DEFAULT_GC_BIAS_PROFILE_150",\n" + | ^ +pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n" + | ^ +pirs_simulate.cpp:672:25: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n", + | ^ +pirs_simulate.cpp:700:30: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 700 | info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t", + | ^ +pirs_simulate.cpp:1235:38: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", + | ^ +pirs_simulate.cpp:1235:57: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", + | ^ +pirs_simulate.cpp:1540:35: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second); + | ^ +pirs_simulate.cpp:1557:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1557 | "# The total number of read pairs that were simulated was %"PRIu64".\n" + | ^ +pirs_simulate.cpp:1574:34: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1574 | error_log.printf("%d\t%"PRIu64"\t%g\n", + | ^ +pirs_simulate.cpp:1579:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1579 | error_log.printf("total\t%"PRIu64"\t%g\n", + | ^ +pirs_simulate.cpp:1685:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1685 | log_parameter(info_log, "Random seed: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1713:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1713 | info("Program: "PROGRAM "\n"); + | ^ +pirs_simulate.cpp:1714:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1714 | info("Version: "VERSION "\n"); + | ^ +pirs_simulate.cpp:1715:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1715 | info("Author: "AUTHOR "\n"); + | ^ +pirs_simulate.cpp:1716:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1716 | info("Contact: "CONTACT "\n"); + | ^ +pirs_simulate.cpp:1717:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^ +pirs_simulate.cpp:1717:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^~~~~~~~ +pirs_simulate.cpp:1717:51: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^~~~~~~~ +pirs_simulate.cpp:1764:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1764 | info("Bases in reference sequences: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1766:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1766 | info("Read pairs simulated: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1768:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1768 | info("Bases in reads: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1773:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1773 | info("Substitution error count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1777:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1777 | info("Insertion count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1779:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1779 | info("Deletion count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1795:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases); + | ^ +pirs_simulate.cpp:1856:22: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1856 | info("Note: A random seed (%"PRIu64") was specified on the command line.\n", + | ^ In file included from SimulationParameters.h:6, from BaseCallingProfile.h:7, from pirs_simulate.cpp:14: @@ -827,7 +863,7 @@ make[3]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' dh_auto_build --sourcedirectory=src/stator/gcContCvgBias -- CC='$(CXX)' - cd src/stator/gcContCvgBias && make -j22 "INSTALL=install --strip-program=true" CC=\$\(CXX\) + cd src/stator/gcContCvgBias && make -j10 "INSTALL=install --strip-program=true" CC=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal self_util.cpp self_util.h g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal main.cpp @@ -853,7 +889,7 @@ make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg' dh_auto_test -O--sourcedirectory=src - cd src && make -j22 check "TESTSUITEFLAGS=-j22 --verbose" VERBOSE=1 + cd src && make -j10 check "TESTSUITEFLAGS=-j10 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' Making check in pirs make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/pirs' @@ -935,12 +971,14 @@ 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/5180/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5180/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/38136 and its subdirectories -I: Current time: Tue Apr 21 13:19:30 -12 2026 -I: pbuilder-time-stamp: 1776820770 +I: removing directory /srv/workspace/pbuilder/5180 and its subdirectories +I: Current time: Thu Mar 20 08:58:01 +14 2025 +I: pbuilder-time-stamp: 1742410681