Diff of the two buildlogs: -- --- b1/build.log 2025-01-28 14:41:11.520508521 +0000 +++ b2/build.log 2025-01-28 14:45:39.740421956 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 28 02:39:42 -12 2025 -I: pbuilder-time-stamp: 1738075182 +I: Current time: Tue Mar 3 11:04:14 +14 2026 +I: pbuilder-time-stamp: 1772485454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking veryfasttree_4.0.4+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2650628/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3105765/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 2 21:04 /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/3105765/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3105765/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='8d6d57acc2db4a62b9f723bd5a4c0312' - 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='2650628' - PS1='# ' - PS2='> ' + INVOCATION_ID=727873e78f874558818061487ddb18c8 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3105765 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.OrpzhKah/pbuilderrc_6cIH --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.OrpzhKah/b1 --logfile b1/build.log veryfasttree_4.0.4+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.OrpzhKah/pbuilderrc_wwKf --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.OrpzhKah/b2 --logfile b2/build.log veryfasttree_4.0.4+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2650628/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3105765/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -180,7 +212,7 @@ Get: 63 http://deb.debian.org/debian unstable/main arm64 libxxhash-dev arm64 0.8.3-2 [82.6 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 robin-map-dev all 1.3.0-1 [29.8 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 49.5 MB in 0s (218 MB/s) +Fetched 49.5 MB in 0s (119 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:arm64. (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 ... 19957 files and directories currently installed.) @@ -455,7 +487,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/veryfasttree-4.0.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../veryfasttree_4.0.4+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3105765/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3105765/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/veryfasttree-4.0.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../veryfasttree_4.0.4+dfsg-1_source.changes dpkg-buildpackage: info: source package veryfasttree dpkg-buildpackage: info: source version 4.0.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -494,7 +530,7 @@ -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") --- Configuring done (1.8s) +-- Configuring done (3.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -526,34 +562,34 @@ make -f CMakeFiles/VeryFastTree.dir/build.make CMakeFiles/VeryFastTree.dir/build make[4]: Entering directory '/build/reproducible-path/veryfasttree-4.0.4+dfsg/obj-aarch64-linux-gnu' [ 6%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDouble.cpp.o -[ 12%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o -[ 18%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o +[ 12%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDouble.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDouble.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDouble.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/VeryFastTreeDouble.cpp -[ 25%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleCuda.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/VeryFastTreeDoubleAVX256.cpp -[ 31%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloat.cpp.o +[ 18%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/VeryFastTreeDoubleAVX512.cpp -[ 37%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleSSE128.cpp.o +[ 25%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleCuda.cpp.o +[ 31%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleSSE128.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatAVX512.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatAVX512.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatAVX512.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/VeryFastTreeFloatAVX512.cpp [ 62%] Building CXX object CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatSSE128.cpp.o +[ 68%] Building CXX object CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. 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CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatSSE128.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatSSE128.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatSSE128.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/VeryFastTreeFloatSSE128.cpp -[ 68%] Building CXX object CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o +/usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/Knuth.cpp [ 75%] Building CXX object CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o +/usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/DiskMemory.cpp [ 81%] Building CXX object CMakeFiles/VeryFastTree.dir/src/Alignment.cpp.o [ 87%] Building CXX object CMakeFiles/VeryFastTree.dir/src/VeryFastTree.cpp.o -/usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/Knuth.cpp -[ 93%] Building CXX object CMakeFiles/VeryFastTree.dir/main.cpp.o -/usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/DiskMemory.cpp /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/Alignment.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/Alignment.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/Alignment.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/Alignment.cpp /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/src/VeryFastTree.cpp.o -MF CMakeFiles/VeryFastTree.dir/src/VeryFastTree.cpp.o.d -o CMakeFiles/VeryFastTree.dir/src/VeryFastTree.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/VeryFastTree.cpp +[ 93%] Building CXX object CMakeFiles/VeryFastTree.dir/main.cpp.o /usr/bin/c++ -DCLI11_BOOST_OPTIONAL=0 -DNDEBUG -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/CLI11/include -I/build/reproducible-path/veryfasttree-4.0.4+dfsg/libs/bxzstr/include -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -std=gnu++11 -fopenmp -MD -MT CMakeFiles/VeryFastTree.dir/main.cpp.o -MF CMakeFiles/VeryFastTree.dir/main.cpp.o.d -o CMakeFiles/VeryFastTree.dir/main.cpp.o -c /build/reproducible-path/veryfasttree-4.0.4+dfsg/main.cpp In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, @@ -609,78 +645,6 @@ /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:5626:23: note: declared here 5626 | std::list tendency; | ^~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1670:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1670:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1671:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1671:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1699:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1699:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1715:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1715:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1732:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1732:17: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ -In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, - inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1748:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] - 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); - | ^~~~ -In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', - inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1748:13: -/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' - 16 | codes = new char[nPos]; - | ^~~~~~~~~~~~~~ In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = float; Operations = veryfasttree::BasicOperations]', inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = float; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = float; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, @@ -753,6 +717,78 @@ /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 2305843009213693951] allocated by 'operator new []' 16 | codes = new char[nPos]; | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1670:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1670:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1671:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1671:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1699:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1699:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1715:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1715:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1732:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1732:17: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ +In member function 'void veryfasttree::NeighbourJoining::Profile::setVectorSize(size_t, veryfasttree::NeighbourJoining::numeric_t, bool) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'void veryfasttree::NeighbourJoining::Profile::reset() [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:175:18, + inlined from 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:26:10, + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1748:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:104:24: warning: array subscript -1 is outside array bounds of 'void [1152921504606846975]' [-Warray-bounds=] + 104 | DynDiskMemory *disk = (DynDiskMemory * ) * (((uintptr_t *) codes) - 1); + | ^~~~ +In constructor 'veryfasttree::NeighbourJoining::Profile::Profile(int64_t, int64_t) [with Precision = double; Operations = veryfasttree::BasicOperations]', + inlined from 'double veryfasttree::NeighbourJoining::MLQuartetOptimize(Profile&, Profile&, Profile&, Profile&, double*, bool*, double*) [with Precision = double; Operations = veryfasttree::BasicOperations]' at /build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:1748:13: +/build/reproducible-path/veryfasttree-4.0.4+dfsg/src/impl/../NeighbourJoining.tcc:16:13: note: at offset -8 into object of size [0, 1152921504606846975] allocated by 'operator new []' + 16 | codes = new char[nPos]; + | ^~~~~~~~~~~~~~ [100%] Linking CXX executable VeryFastTree /usr/bin/cmake -E cmake_link_script CMakeFiles/VeryFastTree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/veryfasttree-4.0.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -DUSE_CUDA=0 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/VeryFastTree.dir/link.d CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDouble.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX256.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleAVX512.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleCuda.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeDoubleSSE128.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloat.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatAVX256.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatAVX512.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatCuda.cpp.o CMakeFiles/VeryFastTree.dir/src/impl/VeryFastTreeFloatSSE128.cpp.o CMakeFiles/VeryFastTree.dir/src/Knuth.cpp.o CMakeFiles/VeryFastTree.dir/src/DiskMemory.cpp.o 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subdirectories +I: Current time: Tue Mar 3 11:08:38 +14 2026 +I: pbuilder-time-stamp: 1772485718