Diff of the two buildlogs: -- --- b1/build.log 2025-01-18 07:33:14.955152984 +0000 +++ b2/build.log 2025-01-18 07:36:36.402061895 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 17 19:30:18 -12 2025 -I: pbuilder-time-stamp: 1737185418 +I: Current time: Sat Feb 21 03:56:18 +14 2026 +I: pbuilder-time-stamp: 1771595778 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,54 +26,86 @@ dpkg-source: info: applying non_x86_malloc I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/35897/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/48673/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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 Feb 20 13:56 /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/48673/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/48673/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=11 ' - 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=21 ' + 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='4753285926a04bb89345167e49a5f4d2' - 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='35897' - PS1='# ' - PS2='> ' + INVOCATION_ID=d385c5c77333419cb770a8c5ba0db07f + 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=48673 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.mxLndY3H/pbuilderrc_WRwk --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.mxLndY3H/b1 --logfile b1/build.log bio-eagle_2.4.1-3.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://46.16.76.132:3128' + 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.mxLndY3H/pbuilderrc_3Xvm --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.mxLndY3H/b2 --logfile b2/build.log bio-eagle_2.4.1-3.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://213.165.73.152:3128 I: uname -a - Linux ionos2-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/35897/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/48673/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -231,7 +263,7 @@ Get: 108 http://deb.debian.org/debian unstable/main i386 libopenblas0 i386 0.3.28+ds-4 [41.0 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libopenblas-pthread-dev i386 0.3.28+ds-4 [3541 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libopenblas-dev i386 0.3.28+ds-4 [54.5 kB] -Fetched 73.6 MB in 2s (31.3 MB/s) +Fetched 73.6 MB in 3s (25.2 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 ... 19837 files and directories currently installed.) @@ -692,7 +724,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bio-eagle-2.4.1/ && 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 > ../bio-eagle_2.4.1-3_source.changes +I: user script /srv/workspace/pbuilder/48673/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/48673/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bio-eagle-2.4.1/ && 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 > ../bio-eagle_2.4.1-3_source.changes dpkg-buildpackage: info: source package bio-eagle dpkg-buildpackage: info: source version 2.4.1-3 dpkg-buildpackage: info: source distribution unstable @@ -702,7 +738,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j11 clean + cd src && make -j21 clean make[1]: Entering directory '/build/reproducible-path/bio-eagle-2.4.1/src' rm -f *.o rm -f eagle @@ -715,28 +751,27 @@ dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src -Nbio-eagle-examples dh_auto_build -O--sourcedirectory=src -Nbio-eagle-examples - cd src && make -j11 "INSTALL=install --strip-program=true" + cd src && make -j21 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bio-eagle-2.4.1/src' g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleMain.o -c EagleMain.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o DipTreePBWT.o -c DipTreePBWT.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Eagle.o -c Eagle.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleImpMiss.o -c EagleImpMiss.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleParams.o -c EagleParams.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EaglePBWT.o -c EaglePBWT.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o FileUtils.o -c FileUtils.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o GenoData.o -c GenoData.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o HapHedge.o -c HapHedge.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MapInterpolater.o -c MapInterpolater.cpp -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MemoryUtils.o -c MemoryUtils.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EaglePBWT.o -c EaglePBWT.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o FileUtils.o -c FileUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o GenoData.o -c GenoData.cpp +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o HapHedge.o -c HapHedge.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MapInterpolater.o -c MapInterpolater.cpp +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MemoryUtils.o -c MemoryUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o NumericUtils.o -c NumericUtils.cpp @@ -744,23 +779,12 @@ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StaticMultimap.o -c StaticMultimap.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StringUtils.o -c StringUtils.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)': -EagleMain.cpp:109:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable] - 109 | HapBitsT *hapBitsTptr = NULL; - | ^~~~~~~~~~~ -EagleMain.cpp:110:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable] - 110 | HapHedge *hapHedgePtr = NULL; - | ^~~~~~~~~~~ -EagleMain.cpp:104:25: warning: unused variable 'timeImpMissing' [-Wunused-variable] - 104 | double timeMN2 = 0, timeImpMissing = 0; - | ^~~~~~~~~~~~~~ -EagleMain.cpp: In function 'int main(int, char**)': -EagleMain.cpp:448:68: warning: unused variable 'timeImpMissing' [-Wunused-variable] - 448 | double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0; - | ^~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o SyncedVcfData.o -c SyncedVcfData.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Timer.o -c Timer.cpp +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ SyncedVcfData.cpp: In member function 'std::vector > EAGLE::SyncedVcfData::processVcfs(const std::string&, const std::string&, const std::string&, bool, int&, int, double, double, std::vector&, std::vector&, const std::string&, const std::string&, int, std::vector > >&, bool, std::vector&)': SyncedVcfData.cpp:228:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 228 | bcf_hdr_write(out, tgt_hdr); @@ -786,6 +810,33 @@ SyncedVcfData.cpp:377:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 377 | bcf_write(out, tgt_hdr, tgt); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)': +EagleMain.cpp:109:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable] + 109 | HapBitsT *hapBitsTptr = NULL; + | ^~~~~~~~~~~ +EagleMain.cpp:110:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable] + 110 | HapHedge *hapHedgePtr = NULL; + | ^~~~~~~~~~~ +EagleMain.cpp:104:25: warning: unused variable 'timeImpMissing' [-Wunused-variable] + 104 | double timeMN2 = 0, timeImpMissing = 0; + | ^~~~~~~~~~~~~~ +EagleMain.cpp: In function 'int main(int, char**)': +EagleMain.cpp:448:68: warning: unused variable 'timeImpMissing' [-Wunused-variable] + 448 | double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0; + | ^~~~~~~~~~~~~~ +SyncedVcfData.cpp: In function 'void EAGLE::process_ref_genotypes(int, int, int32_t*, bool, bool, std::vector&, int&, int&, uint&)': +SyncedVcfData.cpp:103:28: warning: 'haps' may be used uninitialized [-Wmaybe-uninitialized] + 103 | haps[1] = !haps[1]; + | ~~~~~~^ +SyncedVcfData.cpp:60:14: note: 'haps' declared here + 60 | bool haps[2]; bool missing = false, unphased = false; + | ^~~~ +SyncedVcfData.cpp:102:28: warning: 'haps' may be used uninitialized [-Wmaybe-uninitialized] + 102 | haps[0] = !haps[0]; + | ~~~~~~^ +SyncedVcfData.cpp:60:14: note: 'haps' declared here + 60 | bool haps[2]; bool missing = false, unphased = false; + | ^~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::readPhaseConfs(const std::string&)': Eagle.cpp:3108:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3108 | fread(phaseConfs, 1, 2*N*Mseg64*64, fout); @@ -814,21 +865,6 @@ Eagle.cpp:3467:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3467 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Timer.o -c Timer.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -SyncedVcfData.cpp: In function 'void EAGLE::process_ref_genotypes(int, int, int32_t*, bool, bool, std::vector&, int&, int&, uint&)': -SyncedVcfData.cpp:103:28: warning: 'haps' may be used uninitialized [-Wmaybe-uninitialized] - 103 | haps[1] = !haps[1]; - | ~~~~~~^ -SyncedVcfData.cpp:60:14: note: 'haps' declared here - 60 | bool haps[2]; bool missing = false, unphased = false; - | ^~~~ -SyncedVcfData.cpp:102:28: warning: 'haps' may be used uninitialized [-Wmaybe-uninitialized] - 102 | haps[0] = !haps[0]; - | ~~~~~~^ -SyncedVcfData.cpp:60:14: note: 'haps' declared here - 60 | bool haps[2]; bool missing = false, unphased = false; - | ^~~~ Eagle.cpp: In member function 'std::string EAGLE::Eagle::computePhaseString(uint64, uint64, uint64, const std::vector&, const std::vector&, uint64, double, bool) const': Eagle.cpp:1124:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1124 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); @@ -912,8 +948,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'bio-eagle' in '../bio-eagle_2.4.1-3_i386.deb'. -dpkg-deb: building package 'bio-eagle-examples' in '../bio-eagle-examples_2.4.1-3_all.deb'. dpkg-deb: building package 'bio-eagle-dbgsym' in '../bio-eagle-dbgsym_2.4.1-3_i386.deb'. +dpkg-deb: building package 'bio-eagle-examples' in '../bio-eagle-examples_2.4.1-3_all.deb'. dpkg-genbuildinfo --build=binary -O../bio-eagle_2.4.1-3_i386.buildinfo dpkg-genchanges --build=binary -O../bio-eagle_2.4.1-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -921,12 +957,14 @@ 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/48673/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/48673/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/35897 and its subdirectories -I: Current time: Fri Jan 17 19:33:14 -12 2025 -I: pbuilder-time-stamp: 1737185594 +I: removing directory /srv/workspace/pbuilder/48673 and its subdirectories +I: Current time: Sat Feb 21 03:59:34 +14 2026 +I: pbuilder-time-stamp: 1771595974