Diff of the two buildlogs: -- --- b1/build.log 2024-04-28 00:01:08.558204739 +0000 +++ b2/build.log 2024-04-28 00:01:46.752575251 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 27 12:00:22 -12 2024 -I: pbuilder-time-stamp: 1714262422 +I: Current time: Sat May 31 20:24:13 +14 2025 +I: pbuilder-time-stamp: 1748672653 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/15242/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/47827/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 May 31 06:24 /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/47827/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/47827/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='trixie' - 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(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=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='68145e713c01494685196887fdd1bc98' - 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='15242' - PS1='# ' - PS2='> ' + INVOCATION_ID=05592d7e37624ab19c6437314f8a1c26 + 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=47827 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.yrjhj1I6/pbuilderrc_nxno --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.yrjhj1I6/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.yrjhj1I6/pbuilderrc_5wbW --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.yrjhj1I6/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 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:13 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/15242/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/47827/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -154,7 +186,7 @@ Get: 34 http://deb.debian.org/debian trixie/main i386 qt5-qmake-bin i386 5.15.10+dfsg-7 [1123 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 qtchooser i386 66-2 [27.8 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 qt5-qmake i386 5.15.10+dfsg-7 [222 kB] -Fetched 22.9 MB in 1s (29.7 MB/s) +Fetched 22.9 MB in 0s (92.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19884 files and directories currently installed.) @@ -313,7 +345,11 @@ 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/47827/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/47827/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 @@ -339,7 +375,7 @@ 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 @@ -352,10 +388,28 @@ 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/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); + | ~~~~~~^~~~~~~~~~~~~~~~ +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/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') | ~~^~~~~ +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/alignment.cpp: In member function 'void wb::Alignment::writeToFile(char*)': src/alignment.cpp:236:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 236 | char * lets="ATCG"; @@ -372,19 +426,15 @@ src/alignment.cpp:246:38: warning: embedded '\0' in format [-Wformat-contains-nul] 246 | sprintf(buf+end-beg,"\0"); | ^~ -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); - | ~~~~~~^~~~~~~~~~~~~~~~ -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/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)': 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_nu.o src/move_nu.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_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 +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_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) @@ -457,6 +478,20 @@ 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 -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 +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_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_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_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) {} @@ -465,11 +500,49 @@ 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_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) {} - | ~~~~~~~~^ -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/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) { + | ~~~~^ +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 +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