Diff of the two buildlogs: -- --- b1/build.log 2025-03-16 09:11:47.205031075 +0000 +++ b2/build.log 2025-03-16 09:13:00.037734255 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 18 03:34:04 -12 2026 -I: pbuilder-time-stamp: 1776526444 +I: Current time: Sun Mar 16 23:11:49 +14 2025 +I: pbuilder-time-stamp: 1742116309 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/2308642/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2279852/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 16 09:12 /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/2279852/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2279852/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ddbc45202a2547bb89a664ce0a21f4dc' - 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='2308642' - PS1='# ' - PS2='> ' + INVOCATION_ID=39060b419a6a436c8df9dc1521ed3561 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2279852 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.OKcY4Tqf/pbuilderrc_Gr9F --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OKcY4Tqf/b1 --logfile b1/build.log clonalframe_1.2-11.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.OKcY4Tqf/pbuilderrc_TbWO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OKcY4Tqf/b2 --logfile b2/build.log clonalframe_1.2-11.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) 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/2308642/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2279852/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 34 http://deb.debian.org/debian trixie/main amd64 qt5-qmake-bin amd64 5.15.15+dfsg-4+b1 [1067 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 qt5-qmake amd64 5.15.15+dfsg-4+b1 [224 kB] -Fetched 24.2 MB in 0s (107 MB/s) +Fetched 24.2 MB in 0s (51.3 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 ... 19803 files and directories currently installed.) @@ -306,7 +338,11 @@ 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/2279852/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2279852/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 @@ -332,7 +368,7 @@ 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 -j42 + make -j20 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp @@ -354,17 +390,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.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') - | ~~^~~~~ src/genes.cpp: In constructor 'wb::Genes::Genes(wb::Alignment*, char*, char*)': src/genes.cpp:34:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fscanf(mapf,"%d",&buf); @@ -372,13 +397,6 @@ src/genes.cpp:53:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | fscanf(genes,"%d %d",&f1,&f2); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)': -src/util.cpp:83:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 83 | for (unsigned int i=0;i='0' & ch<='9') + | ~~^~~~~ src/alignment_xmfa.cpp: In member function 'void wb::Alignment_xmfa::Fgets(char*, int, FILE*)': src/alignment_xmfa.cpp:187:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 187 | fgets(buf,l,f); @@ -412,10 +435,47 @@ src/alignment_xmfa.cpp:189:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fgets(buf,l,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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.cpp 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.cpp +src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)': +src/burst.cpp:170:28: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector >::size_type' {aka 'long unsigned int'} [-Wformat=] + 170 | printf("Nb groups=%d\n",groups->size()); + | ~^ ~~~~~~~~~~~~~~ + | | | + | int std::vector >::size_type {aka long unsigned int} + | %ld +src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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 'long 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 'long 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 'long unsigned int'} [-Wsign-compare] + 51 | if (l>=t->recMap->size) break; + | ~^~~~~~~~~~~~~~~~~ +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp 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) @@ -443,36 +503,19 @@ src/move_hidden.cpp:203:17: warning: unused variable 'd' [-Wunused-variable] 203 | int d=gsl_vector_int_get(p->a->polySites,old)- gsl_vector_int_get(p->a->polySites,old-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp +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_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) {} - | ~~~~~~~~^ 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/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; - | ^~~~~~~~ -src/ClonalFrame.cpp: In function 'int main(int, char**)': -src/ClonalFrame.cpp:263:53: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 263 | if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");} - | ^~~~~~~~~~~~~~~ -src/ClonalFrame.cpp:341:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] - 341 | printf("Time spent in MH in seconds:%d\n",t2-t); - | ~^ ~~~~ - | | | - | int long unsigned int - | %ld -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/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) {} @@ -481,42 +524,36 @@ 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/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/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_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/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 'long 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:170:28: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector >::size_type' {aka 'long unsigned int'} [-Wformat=] - 170 | printf("Nb groups=%d\n",groups->size()); - | ~^ ~~~~~~~~~~~~~~ - | | | - | int std::vector >::size_type {aka long unsigned int} - | %ld -src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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 'long 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 'long 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/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)': +src/util.cpp:83:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 83 | for (unsigned int i=0;i::__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:575:17, + 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*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/gsl/gsl_errno.h:23, from /usr/include/gsl/gsl_matrix_complex_long_double.h:25, @@ -534,6 +571,24 @@ src/move_hidden.cpp:244:16: note: 'r' was declared here 244 | double r; | ^ +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:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable] + 83 | long int rng_seed; + | ^~~~~~~~ +src/ClonalFrame.cpp: In function 'int main(int, char**)': +src/ClonalFrame.cpp:263:53: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 263 | if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");} + | ^~~~~~~~~~~~~~~ +src/ClonalFrame.cpp:341:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] + 341 | printf("Time spent in MH in seconds:%d\n",t2-t); + | ~^ ~~~~ + | | | + | int long unsigned int + | %ld 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++;} @@ -547,29 +602,10 @@ 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:575:17, - 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*, long 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: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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -604,12 +640,14 @@ 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/2279852/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2279852/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/2308642 and its subdirectories -I: Current time: Sat Apr 18 03:34:46 -12 2026 -I: pbuilder-time-stamp: 1776526486 +I: removing directory /srv/workspace/pbuilder/2279852 and its subdirectories +I: Current time: Sun Mar 16 23:12:59 +14 2025 +I: pbuilder-time-stamp: 1742116379