Diff of the two buildlogs: -- --- b1/build.log 2024-12-16 11:44:27.107355113 +0000 +++ b2/build.log 2024-12-16 11:51:07.297135925 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 15 23:40:57 -12 2024 -I: pbuilder-time-stamp: 1734349257 +I: Current time: Tue Dec 17 01:44:58 +14 2024 +I: pbuilder-time-stamp: 1734349498 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21819/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1333/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4a. +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 Dec 16 11:45 /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/1333/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1333/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='4691a6187cf34706ade87d41bf0b85f1' - 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='21819' - PS1='# ' - PS2='> ' + INVOCATION_ID=f94408a7aa294559be35a2c598e497ab + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=1333 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.1rCjmHns/pbuilderrc_v4MV --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.1rCjmHns/b1 --logfile b1/build.log pirs_2.0.2+dfsg-12.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.1rCjmHns/pbuilderrc_pPHi --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.1rCjmHns/b2 --logfile b2/build.log pirs_2.0.2+dfsg-12.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-23-armmp #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21819/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1333/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: 32 http://deb.debian.org/debian unstable/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-2+b1 [6868 B] Get: 33 http://deb.debian.org/debian unstable/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-2+b1 [7216 B] Get: 34 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] -Fetched 30.6 MB in 1s (30.7 MB/s) +Fetched 30.6 MB in 2s (13.2 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 ... 19680 files and directories currently installed.) @@ -305,7 +337,11 @@ 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/1333/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1333/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 @@ -397,7 +433,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg' dh_auto_build - cd src && make -j3 + cd src && make -j4 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' @@ -406,6 +442,7 @@ g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o InputStream.o InputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o OutputStream.o OutputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o util.o util.cpp main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ @@ -417,16 +454,6 @@ 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 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] @@ -435,6 +462,9 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ 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)); @@ -442,31 +472,13 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o util.o util.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o mt19937-64.o mt19937-64.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o pirs_diploid.o pirs_diploid.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o BaseCallingProfile.o BaseCallingProfile.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", - | ^ -pirs_diploid.cpp:640:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", - | ^ -pirs_diploid.cpp:640:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", - | ^ -pirs_diploid.cpp:642:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", - | ^ -pirs_diploid.cpp:642:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", - | ^ -pirs_diploid.cpp:642:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", - | ^ -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]); - | ^ +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] @@ -498,7 +510,35 @@ | | size_t {aka unsigned int} | long unsigned int | %u -In file included from pirs_diploid.cpp:12: +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o mt19937-64.o mt19937-64.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o pirs_diploid.o pirs_diploid.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o BaseCallingProfile.o BaseCallingProfile.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.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", + | ^ +pirs_diploid.cpp:640:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", + | ^ +pirs_diploid.cpp:640:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", + | ^ +pirs_diploid.cpp:642:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", + | ^ +pirs_diploid.cpp:642:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", + | ^ +pirs_diploid.cpp:642:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", + | ^ +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]); + | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp +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)); @@ -513,7 +553,7 @@ 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)); @@ -528,30 +568,9 @@ 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 BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: + 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)); @@ -581,10 +600,7 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp -In file included from SimulationParameters.h:6, - from GCBiasProfile.h:5, - from GCBiasProfile.cpp:5: +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)); @@ -599,7 +615,7 @@ 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: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)); @@ -614,24 +630,27 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Profile.o Profile.cpp -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 { - | ^~~~~~~~~~~ +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: InputStream.h: In constructor 'InputStream::InputStream()': @@ -693,6 +712,8 @@ | | uint64_t {aka long long unsigned int} | long unsigned int | %llu +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Profile.o Profile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp 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" @@ -781,6 +802,21 @@ 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 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 SimulationParameters.h:6, from BaseCallingProfile.h:7, from pirs_simulate.cpp:14: @@ -831,7 +867,7 @@ 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 -j3 "INSTALL=install --strip-program=true" CC=\$\(CXX\) + cd src/stator/gcContCvgBias && make -j4 "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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal self_util.cpp self_util.h g++ -c -O3 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal main.cpp @@ -1344,7 +1380,7 @@ 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 -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + cd src && make -j4 check "TESTSUITEFLAGS=-j4 --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' @@ -1420,9 +1456,9 @@ dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-12_all.deb'. -dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-12_armhf.deb'. dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-12_armhf.deb'. +dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-12_armhf.deb'. +dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-12_all.deb'. dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-12_all.deb'. dpkg-genbuildinfo --build=binary -O../pirs_2.0.2+dfsg-12_armhf.buildinfo dpkg-genchanges --build=binary -O../pirs_2.0.2+dfsg-12_armhf.changes @@ -1431,12 +1467,14 @@ 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/1333/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1333/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/21819 and its subdirectories -I: Current time: Sun Dec 15 23:44:22 -12 2024 -I: pbuilder-time-stamp: 1734349462 +I: removing directory /srv/workspace/pbuilder/1333 and its subdirectories +I: Current time: Tue Dec 17 01:51:02 +14 2024 +I: pbuilder-time-stamp: 1734349862