Diff of the two buildlogs: -- --- b1/build.log 2025-09-30 14:33:03.182852400 +0000 +++ b2/build.log 2025-09-30 14:36:30.591097295 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 30 02:31:08 -12 2025 -I: pbuilder-time-stamp: 1759242668 +I: Current time: Tue Nov 3 10:56:17 +14 2026 +I: pbuilder-time-stamp: 1793652977 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/391555/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2273927/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 Nov 2 20:56 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2273927/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2273927/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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='75c3264af80f46a5a43f59139fd9b78b' - 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='391555' - PS1='# ' - PS2='> ' + INVOCATION_ID=9a0dcf95021143a2aedc13137c4af967 + 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=2273927 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.IZwxp4qN/pbuilderrc_ZvBT --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.IZwxp4qN/b1 --logfile b1/build.log libbpp-seq_2.4.1-14.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.IZwxp4qN/pbuilderrc_muHg --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.IZwxp4qN/b2 --logfile b2/build.log libbpp-seq_2.4.1-14.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/391555/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2273927/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -176,7 +208,7 @@ Get: 60 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libbpp-core4t64 arm64 2.4.1-14 [534 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbpp-core-dev arm64 2.4.1-14 [922 kB] -Fetched 30.5 MB in 0s (104 MB/s) +Fetched 30.5 MB in 0s (89.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19965 files and directories currently installed.) @@ -444,7 +476,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-14_source.changes +I: user script /srv/workspace/pbuilder/2273927/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2273927/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-14_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-14 dpkg-buildpackage: info: source distribution unstable @@ -471,7 +507,7 @@ -- shared lib: /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (0.4s) +-- Configuring done (0.7s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -490,134 +526,120 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/depend -make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-seq-static.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-seq-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +[ 0%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.cpp -[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.cpp +[ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp -[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -[ 5%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp -[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o +[ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o +[ 4%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 4%] Building CXX object 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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp +[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o 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CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp -[ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o +[ 7%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c 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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp +[ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp -[ 22%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o +[ 19%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -MF 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object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o +[ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong 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-MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp +[ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:49: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 25%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp -[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp -[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp +[ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] @@ -637,121 +659,25 @@ from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 27%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp -[ 28%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp -[ 28%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp -[ 29%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 29%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp -[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:48, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:49: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -761,6 +687,14 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 23%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp +[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: @@ -777,48 +711,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 31%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 31%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp -[ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp -[ 33%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o +[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp -[ 34%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:50, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:51: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 34%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:50, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] @@ -834,8 +728,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 35%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp +[ 26%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40: @@ -851,74 +745,61 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp +[ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp +[ 28%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp +[ 28%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp -[ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp +[ 29%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp +[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp +[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp -[ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp -[ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp -[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -928,68 +809,69 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp -[ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp +[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp +[ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp +[ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] +[ 32%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp +[ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp +[ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp +[ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp +[ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp +[ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:48, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:49: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: +[ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -999,16 +881,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp -[ 41%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp -[ 42%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp -[ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp -[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] @@ -1036,14 +908,24 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp -[ 44%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp -[ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp -[ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 38%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] @@ -1071,35 +953,24 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 72 | v[2] = 50; -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, - inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, - inlined from 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::_ZTv0_n104_NK3bpp34EchinodermMitochondrialGeneticCode18getStopCodonsAsIntEv() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 72 | v[2] = 50; -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 45%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] @@ -1127,113 +998,67 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 46%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o +[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, - inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, - inlined from 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:71:27: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::_ZTv0_n104_NK3bpp36InvertebrateMitochondrialGeneticCode18getStopCodonsAsIntEv() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 46%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o +[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp -[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp -[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp -[ 48%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o +[ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp -[ 48%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o +[ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp -[ 49%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp -[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o +[ 41%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp -[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp +[ 41%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, - inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, - inlined from 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:71:27: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::_ZTv0_n104_NK3bpp28MoldMitochondrialGeneticCode18getStopCodonsAsIntEv() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; -/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1264,18 +1089,54 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o +[ 42%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp +[ 42%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp +[ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:50, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:51: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp -[ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o +[ 44%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp +[ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp -[ 54%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1290,12 +1151,109 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp +[ 45%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp +[ 46%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp +[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp +[ 48%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1310,12 +1268,51 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +[ 51%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1330,12 +1327,18 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp +[ 51%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp +[ 52%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp +[ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp +[ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1350,42 +1353,49 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; +[ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp +[ 54%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp +[ 54%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 72 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, - inlined from 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:71:27: + inlined from 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::_ZTv0_n104_NK3bpp29YeastMitochondrialGeneticCode18getStopCodonsAsIntEv() const': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] - 73 | v[2] = 50; +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::_ZTv0_n104_NK3bpp34EchinodermMitochondrialGeneticCode18getStopCodonsAsIntEv() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 72 | v[2] = 50; /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: +[ 55%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1396,37 +1406,71 @@ 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp -[ 56%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, + inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, + inlined from 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:71:27: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::_ZTv0_n104_NK3bpp36InvertebrateMitochondrialGeneticCode18getStopCodonsAsIntEv() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1439,15 +1483,78 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: +[ 55%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp +[ 56%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPhd.cpp +[ 57%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp +[ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp +[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, + inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, + inlined from 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:71:27: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::_ZTv0_n104_NK3bpp28MoldMitochondrialGeneticCode18getStopCodonsAsIntEv() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 58%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp +[ 59%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp +[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp +[ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/StreamSequenceIterator.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractOAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:45: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1457,16 +1564,20 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp -[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp -[ 58%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp +[ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp +[ 63%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1481,13 +1592,10 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1502,68 +1610,117 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceExceptions.cpp +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/15/bits/alloc_traits.h:614:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:387:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, + inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:341:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, + inlined from 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:71:27: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::_ZTv0_n104_NK3bpp29YeastMitochondrialGeneticCode18getStopCodonsAsIntEv() const': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] + 73 | v[2] = 50; +/usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequencePositionIterators.cpp +[ 65%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp +[ 65%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWalker.cpp +[ 65%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp +[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp +[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotation.cpp +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp: In static member function 'static bpp::Sequence* bpp::SequenceTools::subtractHaplotype(const bpp::Sequence&, const bpp::Sequence&, std::string, unsigned int)': +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:556:13: warning: ignoring return value of '_FIter std::remove(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = int]', declared with attribute 'nodiscard' [-Wunused-result] + 556 | remove(nucs.begin(), nucs.end(), h.getValue(i)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/algorithm:63, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../SymbolList.h:49, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Sequence.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.h:49, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:42: +/usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here + 772 | remove(_ForwardIterator __first, _ForwardIterator __last, + | ^~~~~~ +[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotationTools.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQuality.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp +[ 69%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o +[ 69%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Site.cpp +[ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp +[ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp -[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o +[ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp -[ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 72%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp +[ 72%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43, @@ -1582,6 +1739,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, @@ -1600,43 +1759,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp +[ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, @@ -1655,38 +1779,34 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o +[ 74%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp +[ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp -[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPhd.cpp -[ 65%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o +[ 74%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolList.cpp +[ 75%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp +[ 76%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp -[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp -[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp -[ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.h:43, @@ -1705,90 +1825,76 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 76%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Transliterator.cpp +[ 77%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp +[ 77%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ -[ 68%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o +[ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp +[ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp +[ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPhd.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o +[ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1801,52 +1907,36 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 70%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o +[ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/StreamSequenceIterator.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o +[ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp -[ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o +[ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/StreamSequenceIterator.cpp +[ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp +[ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractOAlignment.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp:42: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:45: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceExceptions.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractOAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.h:43, @@ -1865,60 +1955,29 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -[ 73%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp -[ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp -[ 74%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp -[ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceExceptions.cpp -[ 76%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o 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"CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o" +/usr/bin/ranlib libbpp-seq.a +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +[ 85%] Built target bpp-seq-static +[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -c 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp -[ 82%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp: In static member function 'static bpp::Sequence* bpp::SequenceTools::subtractHaplotype(const bpp::Sequence&, const bpp::Sequence&, std::string, unsigned int)': -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:556:13: warning: ignoring return value of '_FIter std::remove(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = int]', declared with attribute 'nodiscard' [-Wunused-result] - 556 | remove(nucs.begin(), nucs.end(), h.getValue(i)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/algorithm:63, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../SymbolList.h:49, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Sequence.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.h:49, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:42: -/usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here - 772 | remove(_ForwardIterator __first, _ForwardIterator __last, - | ^~~~~~ -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Site.cpp -[ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o +[ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp +[ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Site.cpp /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp: In static member function 'static bpp::Sequence* bpp::SequenceTools::subtractHaplotype(const bpp::Sequence&, const bpp::Sequence&, std::string, unsigned int)': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:556:13: warning: ignoring return value of '_FIter std::remove(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = int]', declared with attribute 'nodiscard' [-Wunused-result] 556 | remove(nucs.begin(), nucs.end(), h.getValue(i)); @@ -1933,41 +1992,18 @@ /usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here 772 | remove(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~ -[ 84%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp -[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp -[ 84%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -c 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o +[ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Transliterator.cpp -[ 91%] Linking CXX static library libbpp-seq.a -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-static.dir/link.txt --verbose=1 -/usr/bin/ar qc libbpp-seq.a "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o" 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test/CMakeFiles/test_sequences.dir/depend -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_containers.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_walker.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build +make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -[ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -MF CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o.d -o CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alphabets.cpp make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build +make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/build +make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -[ 93%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -MF CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o.d -o CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build +make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_bowker.cpp make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build -make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build +make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -[ 94%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_io.dir/test_io.cpp.o -MF CMakeFiles/test_io.dir/test_io.cpp.o.d -o CMakeFiles/test_io.dir/test_io.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp -[ 95%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o -[ 96%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_containers.dir/test_containers.cpp.o -MF CMakeFiles/test_containers.dir/test_containers.cpp.o.d -o CMakeFiles/test_containers.dir/test_containers.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp +[ 95%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_io.dir/test_io.cpp.o -MF CMakeFiles/test_io.dir/test_io.cpp.o.d -o CMakeFiles/test_io.dir/test_io.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp +[ 96%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o +[ 97%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o -MF CMakeFiles/test_sequences.dir/test_sequences.cpp.o.d -o CMakeFiles/test_sequences.dir/test_sequences.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_sequences.cpp -[ 97%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o +[ 97%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -MF CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o.d -o CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alphabets.cpp +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -MF CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o.d -o CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp +[ 98%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_walker.dir/test_walker.cpp.o -MF CMakeFiles/test_walker.dir/test_walker.cpp.o.d -o CMakeFiles/test_walker.dir/test_walker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_walker.cpp -[ 98%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_bowker.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp:41: + from /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ @@ -2055,66 +2091,66 @@ from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp:41: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] - 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; - | ^~~~~~~~ -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' - 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; - | ^~~~~~~~ + from /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] + 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' + 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; + | ^~~~~~~~ [ 98%] Linking CXX executable test_containers cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.dir/link.txt --verbose=1 -[ 98%] Linking CXX executable test_alphabets -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Linking CXX executable test_walker cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_walker.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_containers -[ 99%] Linking CXX executable test_bowker -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_walker +[ 99%] Linking CXX executable test_alphabets +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable test_sequences +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequences.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_alphabets -[ 99%] Linking CXX executable test_io -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable test_sequences -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequences.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +[ 99%] Built target test_sequences +[ 99%] Linking CXX executable test_bowker +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' +[ 99%] Linking CXX executable test_io +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.dir/link.txt --verbose=1 [ 99%] Built target test_bowker /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_io -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' -[ 99%] Built target test_sequences [100%] Linking CXX executable test_alignment_scores cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_scores.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 @@ -2182,22 +2218,6 @@ 7: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_walker 7: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 7: Test timeout computed to be: 60000 -1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 -1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 -1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 -1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 -3: 2 0.919699 -1/7 Test #1: test_alignment_scores ............ Passed 0.02 sec -2/7 Test #2: test_alphabets ................... Passed 0.02 sec -4: 47 -4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- -4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- -4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% -4: 30 -4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU -4: GAAGGCGG-GUUUUGCGACCGACG--UUUU -3/7 Test #4: test_containers .................. Passed 0.01 sec 7: 0 A 4 7: 1 U 5 7: 2 G 6 @@ -2240,17 +2260,6 @@ 7: 4 7: 26 7: 44 -6: --- Strict match --- -6: ATTT: 0 -6: TCG: 3 -6: GATC: 29 -6: CGTC: 33 -6: CWCAT: 19 -6: --- Degenerated match --- -6: CTCAT: 19 -6: AAGCA: 16 -5: example.fasta contains 100 sequences -4/7 Test #6: test_sequences ................... Passed 0.01 sec 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: _________________________________________________ 7: 0 - 0 @@ -2316,20 +2325,47 @@ 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% +4: 47 +4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- +4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- +4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% +4: 30 +4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU +4: GAAGGCGG-GUUUUGCGACCGACG--UUUU +3: 2 0.919699 +1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 +1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 +1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 +1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 +6: --- Strict match --- +6: ATTT: 0 +6: TCG: 3 +6: GATC: 29 +6: CGTC: 33 +6: CWCAT: 19 +6: --- Degenerated match --- +6: CTCAT: 19 +6: AAGCA: 16 +1/7 Test #1: test_alignment_scores ............ Passed 0.03 sec +2/7 Test #2: test_alphabets ................... Passed 0.03 sec +3/7 Test #4: test_containers .................. Passed 0.02 sec +4/7 Test #6: test_sequences ................... Passed 0.02 sec 5/7 Test #7: test_walker ...................... Passed 0.02 sec +5: example.fasta contains 100 sequences 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 -6/7 Test #5: test_io .......................... Passed 0.04 sec -3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0094 0.051 0.098 0.5112 -3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0094 0.0524 0.0996 0.4998 -7/7 Test #3: test_bowker ...................... Passed 26.50 sec +6/7 Test #5: test_io .......................... Passed 0.05 sec +3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0104 0.0468 0.095 0.495 +3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.01 0.0572 0.107 0.5092 +7/7 Test #3: test_bowker ...................... Passed 40.01 sec 100% tests passed, 0 tests failed out of 7 -Total Test time (real) = 26.51 sec +Total Test time (real) = 40.03 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -2536,8 +2572,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-14_arm64.deb'. dpkg-deb: building package 'libbpp-seq-dev' in '../libbpp-seq-dev_2.4.1-14_arm64.deb'. +dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-14_arm64.deb'. dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-14_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-14_arm64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-14_arm64.changes @@ -2546,12 +2582,14 @@ 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/2273927/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2273927/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/391555 and its subdirectories -I: Current time: Tue Sep 30 02:33:00 -12 2025 -I: pbuilder-time-stamp: 1759242780 +I: removing directory /srv/workspace/pbuilder/2273927 and its subdirectories +I: Current time: Tue Nov 3 10:59:29 +14 2026 +I: pbuilder-time-stamp: 1793653169