Diff of the two buildlogs: -- --- b1/build.log 2024-12-23 02:38:15.403330370 +0000 +++ b2/build.log 2024-12-23 02:38:52.821636293 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 22 14:34:40 -12 2024 -I: pbuilder-time-stamp: 1734921280 +I: Current time: Sun Jan 25 23:01:21 +14 2026 +I: pbuilder-time-stamp: 1769331681 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying glibc2.27.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/49415/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/53343/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 Jan 25 09:01 /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/53343/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/53343/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='20fa856ae2c34240a7b0bfcf2a27be3f' - 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='49415' - PS1='# ' - PS2='> ' + INVOCATION_ID=187fddf88c0a4cb3bace657814f2bd5c + 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=53343 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.RW2iIKa7/pbuilderrc_hf5E --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.RW2iIKa7/b1 --logfile b1/build.log clonalframe_1.2-11.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.RW2iIKa7/pbuilderrc_SKFT --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.RW2iIKa7/b2 --logfile b2/build.log clonalframe_1.2-11.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 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) 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/49415/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/53343/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -153,7 +185,7 @@ Get: 33 http://deb.debian.org/debian unstable/main i386 qt5-qmake-bin i386 5.15.15+dfsg-2 [1142 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 qtchooser i386 66-2 [27.8 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 qt5-qmake i386 5.15.15+dfsg-2 [224 kB] -Fetched 23.8 MB in 4s (6206 kB/s) +Fetched 23.8 MB in 1s (22.4 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 ... 19953 files and directories currently installed.) @@ -308,7 +340,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/clonalframe-1.2/ && 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 > ../clonalframe_1.2-11_source.changes +I: user script /srv/workspace/pbuilder/53343/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/53343/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/clonalframe-1.2/ && 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 > ../clonalframe_1.2-11_source.changes dpkg-buildpackage: info: source package clonalframe dpkg-buildpackage: info: source version 1.2-11 dpkg-buildpackage: info: source distribution unstable @@ -334,7 +370,7 @@ Info: creating stash file /build/reproducible-path/clonalframe-1.2/.qmake.stash make[1]: Leaving directory '/build/reproducible-path/clonalframe-1.2' dh_auto_build - make -j11 + make -j21 make[1]: Entering directory '/build/reproducible-path/clonalframe-1.2' g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment_xmfa.o src/alignment_xmfa.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp @@ -347,6 +383,16 @@ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_ages.o src/move_ages.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_delta.o src/move_delta.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_gap.o src/move_gap.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_hidden.o src/move_hidden.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_hidden2.o src/move_hidden2.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move.o src/move.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/param.o src/param.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/recorder.o src/recorder.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.cpp src/alignment_structure.cpp: In constructor 'wb::Alignment_structure::Alignment_structure(char*, int)': src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 45 | if (ch>='0' & ch<='9') @@ -378,6 +424,8 @@ src/alignment_xmfa.cpp:129:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 129 | for (j=0;j=t->recMap->size) break; - | ~^~~~~~~~~~~~~~~~~ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.cpp -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.cpp +g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.cpp +src/move_nu.cpp: In constructor 'wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)': +src/move_nu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter] + 24 | Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {} + | ~~~~~~~~^ +src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)': +src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 56 | if (gsl_vector_char_get(t->recMap,j)==1) + | ^ src/move_ages.cpp: In member function 'virtual void wb::Move_ages::move(wb::Param*)': src/move_ages.cpp:60:21: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] 60 | } else ;//printf("Age change rejected because out of range\n"); | ^ -src/move_delta.cpp: In constructor 'wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)': -src/move_delta.cpp:24:50: warning: unused parameter 'p' [-Wunused-parameter] - 24 | Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) { - | ~~~~~~~~^ -src/move_gap.cpp: In constructor 'wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)': -src/move_gap.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter] - 24 | Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {} +src/move_rho.cpp: In constructor 'wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)': +src/move_rho.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter] + 24 | Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng) | ~~~~~~~~^ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.cpp -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.cpp -src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)': -src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 188 | for (k=1;ksize();k++) - | ~^~~~~~~~~~~~ -src/burst.cpp:190:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 190 | if (k>=rid->size()) continue; - | ~^~~~~~~~~~~~~ -src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector >*, int)': -src/burst.cpp:259:42: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 259 | if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) { - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -src/burst.cpp:252:89: warning: unused parameter 'f' [-Wunused-parameter] - 252 | void Burst::optimiseFathers(gsl_vector_int * fathers,vector > *slvs,int f) { - | ~~~~^ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/move.o src/move.cpp -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/param.o src/param.cpp -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/recorder.o src/recorder.cpp -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.cpp -src/move_mu.cpp: In constructor 'wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)': -src/move_mu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter] - 24 | Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {} - | ~~~~~~~~^ src/move_hidden.cpp: In constructor 'wb::Move_hidden::Move_hidden(gsl_rng*, wb::Param*)': src/move_hidden.cpp:25:52: warning: unused parameter 'p' [-Wunused-parameter] 25 | Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng) | ~~~~~~~~^ +src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)': +src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable] + 127 | int sizeys2=propLocs(ys,probys,x,p); + | ^~~~~~~ src/move_hidden.cpp: In member function 'void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)': src/move_hidden.cpp:127:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 127 | for (unsigned int i=0;ia->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1); | ^ -In file included from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3906, - from /usr/include/c++/14/math.h:36, - from /usr/include/gsl/gsl_math.h:22, - from src/alignment.h:25, - from src/burst.h:24, - from src/burst.cpp:20: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, - inlined from 'std::vector >* wb::Burst::makeClusters(std::vector*, gsl_vector_int*, int, bool)' at src/burst.cpp:299:67: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/move_nu.cpp: In constructor 'wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)': -src/move_nu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter] - 24 | Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {} - | ~~~~~~~~^ -src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)': -src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 56 | if (gsl_vector_char_get(t->recMap,j)==1) - | ^ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.cpp -src/move_rho.cpp: In constructor 'wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)': -src/move_rho.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter] - 24 | Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng) +src/move_gap.cpp: In constructor 'wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)': +src/move_gap.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter] + 24 | Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {} | ~~~~~~~~^ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.cpp -src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)': -src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable] - 127 | int sizeys2=propLocs(ys,probys,x,p); - | ^~~~~~~ -g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.cpp +src/move_mu.cpp: In constructor 'wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)': +src/move_mu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter] + 24 | Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {} + | ~~~~~~~~^ +src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)': +src/hashcell.cpp:51:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + 51 | if (l>=t->recMap->size) break; + | ~^~~~~~~~~~~~~~~~~ +src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)': +src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 188 | for (k=1;ksize();k++) + | ~^~~~~~~~~~~~ +src/burst.cpp:190:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 190 | if (k>=rid->size()) continue; + | ~^~~~~~~~~~~~~ +src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector >*, int)': +src/burst.cpp:259:42: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 259 | if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) { + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ +src/burst.cpp:252:89: warning: unused parameter 'f' [-Wunused-parameter] + 252 | void Burst::optimiseFathers(gsl_vector_int * fathers,vector > *slvs,int f) { + | ~~~~^ +src/move_delta.cpp: In constructor 'wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)': +src/move_delta.cpp:24:50: warning: unused parameter 'p' [-Wunused-parameter] + 24 | Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) { + | ~~~~~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree.o src/tree.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp @@ -525,23 +538,29 @@ src/util.cpp:85:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 85 | for (unsigned int i=0;irec++;} - | ~~~^~~~~~~~~ -src/tree.cpp:197:20: note: 'vals[5]' was declared here - 197 | double vals[10]; - | ^~~~ -src/tree.cpp:229:87: warning: 'vals[9]' may be used uninitialized [-Wmaybe-uninitialized] - 229 | } else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;} - | ~~~^~~~~~~~~ -src/tree.cpp:197:20: note: 'vals[9]' was declared here - 197 | double vals[10]; - | ^~~~ +In file included from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3906, + from /usr/include/c++/14/math.h:36, + from /usr/include/gsl/gsl_math.h:22, + from src/alignment.h:25, + from src/burst.h:24, + from src/burst.cpp:20: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, + inlined from 'std::vector >* wb::Burst::makeClusters(std::vector*, gsl_vector_int*, int, bool)' at src/burst.cpp:299:67: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/ClonalFrame.cpp: In function 'gsl_rng* makerng()': src/ClonalFrame.cpp:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable] 83 | long int rng_seed; @@ -556,10 +575,27 @@ | | | | int long unsigned int | %ld +src/tree.cpp: In static member function 'static wb::Tree* wb::Tree::move(wb::Tree*, wb::Tree*, double, gsl_vector_char*, gsl_vector_char*, wb::Param*)': +src/tree.cpp:99:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 99 | if (z!=NULL) + | ^ src/ClonalFrame.cpp: In function 'gsl_rng* makerng()': src/ClonalFrame.cpp:96:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fread(&seed,sizeof(seed),1,devrandom); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/tree.cpp: In member function 'double wb::Tree::llhoodb(wb::Param*)': +src/tree.cpp:223:29: warning: 'vals[5]' may be used uninitialized [-Wmaybe-uninitialized] + 223 | {ret+=vals[5];p->rec++;} + | ~~~^~~~~~~~~ +src/tree.cpp:197:20: note: 'vals[5]' was declared here + 197 | double vals[10]; + | ^~~~ +src/tree.cpp:229:87: warning: 'vals[9]' may be used uninitialized [-Wmaybe-uninitialized] + 229 | } else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;} + | ~~~^~~~~~~~~ +src/tree.cpp:197:20: note: 'vals[9]' was declared here + 197 | double vals[10]; + | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -lgsl -lgslcblas make[1]: Leaving directory '/build/reproducible-path/clonalframe-1.2' dh_auto_test @@ -585,8 +621,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-11_i386.deb'. dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-11_i386.deb'. +dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-11_i386.deb'. dpkg-genbuildinfo --build=binary -O../clonalframe_1.2-11_i386.buildinfo dpkg-genchanges --build=binary -O../clonalframe_1.2-11_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -594,12 +630,14 @@ 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/53343/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/53343/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/49415 and its subdirectories -I: Current time: Sun Dec 22 14:38:13 -12 2024 -I: pbuilder-time-stamp: 1734921494 +I: removing directory /srv/workspace/pbuilder/53343 and its subdirectories +I: Current time: Sun Jan 25 23:01:51 +14 2026 +I: pbuilder-time-stamp: 1769331711