Diff of the two buildlogs: -- --- b1/build.log 2024-09-09 12:40:18.340783537 +0000 +++ b2/build.log 2024-09-09 12:50:15.411409250 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 9 00:34:07 -12 2024 -I: pbuilder-time-stamp: 1725885247 +I: Current time: Tue Sep 10 02:40:47 +14 2024 +I: pbuilder-time-stamp: 1725885647 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6134/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20348/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 Sep 9 12:41 /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/20348/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20348/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='43c0ab72440e4b84a77172fb9bc1b0f7' - 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='6134' - PS1='# ' - PS2='> ' + INVOCATION_ID=73967dd7ba8a4d599a0cc3a0895c3322 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=20348 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.ANDwv3wq/pbuilderrc_jyPO --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ANDwv3wq/b1 --logfile b1/build.log libbpp-seq_2.4.1-13.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.ANDwv3wq/pbuilderrc_Hgra --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ANDwv3wq/b2 --logfile b2/build.log libbpp-seq_2.4.1-13.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64z 6.1.0-25-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-armmp-lpae #1 SMP Debian 6.1.106-3 (2024-08-26) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6134/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/20348/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -172,7 +204,7 @@ Get: 54 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libbpp-core4t64 armhf 2.4.1-13 [525 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libbpp-core-dev armhf 2.4.1-13 [958 kB] -Fetched 31.7 MB in 0s (66.7 MB/s) +Fetched 31.7 MB in 1s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19492 files and directories currently installed.) @@ -411,7 +443,11 @@ Building tag database... -> Finished parsing the build-deps 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_2.4.1-13_source.changes +I: user script /srv/workspace/pbuilder/20348/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/20348/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_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable @@ -446,7 +482,7 @@ -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (0.6s) +-- Configuring done (0.8s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -458,7 +494,7 @@ -- Build files have been written to: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -476,43 +512,57 @@ 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-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 0%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o +[ 2%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/AlphabetExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o +[ 4%] 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/BinaryAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 3%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 4%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o +[ 4%] 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-arm-linux-gnueabihf/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 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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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp -[ 3%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o +[ 7%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 7%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o cd 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp +[ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/IntegerAlphabet.cpp.o -MF 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/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp -[ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o +[ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp +[ 12%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o +[ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp +[ 14%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, @@ -532,8 +582,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void bpp::NumericAlphabet::remap()' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:159:16: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -552,30 +600,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 11%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp -[ 12%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp -[ 12%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp -[ 12%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp -[ 14%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 14%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp -[ 14%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp -[ 16%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp -[ 16%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44, @@ -603,8 +627,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 17%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'virtual void bpp::NumericAlphabet::setState(size_t, bpp::AlphabetState*)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:87:14: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -614,18 +636,38 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp -[ 18%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o +[ 14%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp -[ 19%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 20%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp +[ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp +[ 15%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp +[ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp +[ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o +cd 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-ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp +[ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 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-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp +[ 19%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp +[ 20%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp +[ 20%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 20%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 22%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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=] @@ -643,6 +685,49 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /usr/include/c++/14/map:62, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp:40: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:52, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:49, @@ -654,16 +739,6 @@ /usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp -In file included from /usr/include/c++/14/map:62, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp:40: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static bpp::Site* bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(const bpp::Site&, const bpp::GeneticCode&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp:204:31: @@ -692,45 +767,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 22%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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=] - 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 22%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp -[ 23%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 23%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 24%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/CompressedVectorSiteContainer.h:44, @@ -747,8 +789,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 23%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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: @@ -765,14 +805,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp -[ 25%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp -[ 25%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 25%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 26%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 27%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: @@ -803,16 +841,18 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 26%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 27%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:47: /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 28%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void bpp::SequenceContainerTools::getFrequencies(const bpp::SequenceContainer&, std::map&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:162:15: @@ -832,8 +872,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 27%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 29%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -866,10 +906,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 28%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp -[ 29%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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: @@ -886,6 +922,24 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ +[ 29%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /usr/include/c++/14/map:62, from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, from /usr/include/Bpp/Numeric/Function/Functions.h:45, @@ -896,8 +950,8 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 29%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void bpp::SiteContainerTools::removeGapSites(bpp::SiteContainer&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:334:16: @@ -908,22 +962,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ +[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static bpp::SiteContainer* bpp::SiteContainerTools::removeGapSites(const bpp::SiteContainer&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:321:16: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -933,18 +973,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp -[ 31%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp -[ 31%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 32%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 32%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 31%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 32%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 32%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 33%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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=] @@ -972,12 +1010,14 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 33%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 33%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp +[ 33%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 34%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 34%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 35%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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=] @@ -1005,8 +1045,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 35%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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=] @@ -1034,16 +1072,14 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 35%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 36%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 38%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 35%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 36%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 37%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 38%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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=] @@ -1061,6 +1097,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ +[ 38%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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=] @@ -1099,54 +1137,6 @@ /usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 38%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 39%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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; - | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 39%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 40%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 40%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.h:43, @@ -1155,44 +1145,8 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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: -/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ +[ 38%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static bpp::Site* bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(const bpp::Site&, const bpp::GeneticCode&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp:204:31: @@ -1221,12 +1175,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 41%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 39%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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/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; | ^~~~~~~~ @@ -1241,36 +1195,15 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 42%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 43%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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=] - 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 43%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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: +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; | ^~~~~~~~ +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1280,13 +1213,14 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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/AlignedSequenceContainer.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: +[ 40%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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=] 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1296,75 +1230,57 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 43%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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, - 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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 44%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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=] +[ 40%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 40%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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; | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, 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=] +/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/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 44%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 45%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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: -/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=] +[ 42%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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; | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, 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=] +/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/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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: +[ 42%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 42%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1374,11 +1290,10 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 46%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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/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: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; | ^~~~~~~~ @@ -1393,12 +1308,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 47%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 43%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: + 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: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; | ^~~~~~~~ @@ -1413,14 +1328,23 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 47%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/MaseTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: +[ 44%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 44%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 45%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 45%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1430,32 +1354,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 47%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 48%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/../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: + 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; | ^~~~~~~~ @@ -1468,16 +1372,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 49%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 49%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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: +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1487,16 +1387,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 50%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 51%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: +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; | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1512,8 +1408,8 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 46%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void bpp::SequenceContainerTools::getFrequencies(const bpp::SequenceContainer&, std::map&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:162:15: @@ -1533,12 +1429,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 51%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 52%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 53%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 46%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 47%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 48%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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, @@ -1555,14 +1451,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 53%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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/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: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; | ^~~~~~~~ @@ -1575,15 +1469,33 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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: +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 48%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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; | ^~~~~~~~ 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: + 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1593,15 +1505,15 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 53%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/SiteContainerTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: +[ 49%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1611,10 +1523,26 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 54%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 50%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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: +/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /usr/include/c++/14/map:62, from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, from /usr/include/Bpp/Numeric/Function/Functions.h:45, @@ -1635,8 +1563,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 50%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static bpp::SiteContainer* bpp::SiteContainerTools::removeGapSites(const bpp::SiteContainer&, double)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:321:16: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -1646,23 +1574,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 56%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequencePositionIterators.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWalker.cpp -[ 58%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: +[ 50%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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; | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1672,40 +1592,306 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotation.cpp -[ 59%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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=] +[ 51%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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: +/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/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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/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/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotationTools.cpp -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQuality.cpp -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp -[ 63%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 52%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 52%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 52%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 53%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 53%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 54%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 54%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + 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++/14/bits/alloc_traits.h:478:28, + 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++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + 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++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, + 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 55%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 56%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 56%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 56%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 57%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + 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++/14/bits/alloc_traits.h:478:28, + 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++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + 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++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, + 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: 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-static.dir/Bpp/Seq/Io/Stockholm.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 59%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + 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++/14/bits/alloc_traits.h:478:28, + 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++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + 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++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, + 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 59%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 59%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 61%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-static.dir/Bpp/Seq/SequenceExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 63%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 63%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 65%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + 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++/14/bits/alloc_traits.h:478:28, + 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++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + 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++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, + 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 66%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 67%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 68%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 68%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 69%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 70%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.h:44, @@ -1718,51 +1904,24 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp -In file included from /usr/include/c++/14/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'static double bpp::SiteTools::mutualInformation(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:241:57: -/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'static double bpp::SiteTools::mutualInformation(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:259:57: -/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'static double bpp::SiteTools::jointEntropy(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:286:57: -/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'static double bpp::SiteTools::jointEntropy(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:294:57: -/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolList.cpp -[ 65%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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; + | ^~~~~~~~ +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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -1774,6 +1933,8 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::StringSequenceTools::getGCcontent(const std::string&, size_t, size_t)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp:214:25: @@ -2081,12 +2242,51 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 66%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +In file included from /usr/include/c++/14/map:63: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'static double bpp::SiteTools::mutualInformation(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:241:57: +/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'static double bpp::SiteTools::mutualInformation(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:259:57: +/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'static double bpp::SiteTools::jointEntropy(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:286:57: +/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'static double bpp::SiteTools::jointEntropy(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:294:57: +/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 71%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 71%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 71%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 72%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp:40: @@ -2122,6 +2322,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 72%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void bpp::SymbolListTools::getCounts(const bpp::SymbolList&, const bpp::SymbolList&, std::map >&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp:75:32: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -2140,8 +2342,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 67%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void bpp::SymbolListTools::getFrequencies(const bpp::SymbolList&, const bpp::SymbolList&, std::map >&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp:111:35: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -2151,317 +2351,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 68%] Linking CXX shared library libbpp-seq.so -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-shared.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-seq.so.12 -o libbpp-seq.so.12.0.0 "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o" 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"CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o" /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - 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++/14/bits/alloc_traits.h:478:28, - 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++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - 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++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, - 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-seq.so.12.0.0 libbpp-seq.so.12 libbpp-seq.so -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 68%] Built target bpp-seq-shared -make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_alignment_scores.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: -/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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 69%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 69%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 70%] Linking CXX executable test_alignment_scores -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 70%] Built target test_alignment_scores -make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_alphabets.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 71%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - 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++/14/bits/alloc_traits.h:478:28, - 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++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - 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++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, - 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: 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/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/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - 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++/14/bits/alloc_traits.h:478:28, - 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++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - 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++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, - 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 71%] Linking CXX executable test_alphabets -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 71%] Built target test_alphabets -make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 72%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 73%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 73%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 73%] Linking CXX executable test_bowker -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 73%] Built target test_bowker -make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_containers.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 74%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 74%] Linking CXX executable test_containers -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 74%] Built target test_containers -make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 75%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 76%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 76%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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/test/test_io.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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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; -In file included from /usr/include/arm-linux-gnueabihf/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - 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++/14/bits/alloc_traits.h:478:28, - 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++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - 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++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, - 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++/14/bits/new_allocator.h:151:55: 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_n52_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++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 76%] Linking CXX executable test_io -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 76%] Built target test_io -make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 77%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 78%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 78%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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; - | ^~~~~~~~ -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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' - 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; - | ^~~~~~~~ -[ 78%] Linking CXX executable test_sequences -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 78%] Built target test_sequences -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-arm-linux-gnueabihf' -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_walker.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -[ 79%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 80%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 81%] Linking CXX executable test_walker -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[ 81%] Built target test_walker -[ 81%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 73%] Linking CXX static library libbpp-seq.a +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o" 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"CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "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" 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, @@ -2480,8 +2373,11 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 82%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +/usr/bin/ranlib libbpp-seq.a +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 73%] Built target bpp-seq-static +[ 74%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -2500,10 +2396,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 83%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 83%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 74%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -2522,8 +2416,12 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 84%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 75%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 75%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 76%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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, @@ -2560,8 +2458,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 84%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -2580,10 +2476,8 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 85%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 85%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 76%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -2602,6 +2496,10 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ +[ 77%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 78%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: @@ -2619,10 +2517,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 86%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 86%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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, @@ -2641,6 +2535,10 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ +[ 78%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 79%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/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=] @@ -2656,8 +2554,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 87%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/../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, @@ -2676,14 +2572,16 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 87%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 88%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 88%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 89%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 79%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 80%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp +[ 81%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 81%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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, @@ -2702,10 +2600,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 90%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 90%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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, @@ -2724,34 +2618,49 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ -[ 91%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 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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 -[ 92%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 92%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 93%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 93%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 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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 -[ 95%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 97%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 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-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 -[ 98%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 82%] 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o +cd 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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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequencePositionIterators.cpp +[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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=. 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CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotation.cpp +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotationTools.cpp +[ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQuality.cpp +[ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp +[ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolList.cpp +In file included from /usr/include/c++/14/map:62, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp:42: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.h:44, @@ -2764,17 +2673,6 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/map:62, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp:42: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::StringSequenceTools::getGCcontent(const std::string&, size_t, size_t)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp:214:25: @@ -3082,8 +2980,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 98%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 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-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::SiteTools::mutualInformation(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:241:57: @@ -3103,8 +3003,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 99%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::SiteTools::jointEntropy(const bpp::Site&, const bpp::Site&, bool)' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp:286:57: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -3123,8 +3021,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 99%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp:40: @@ -3187,21 +3083,161 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[100%] Linking CXX static library libbpp-seq.a -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o" 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"CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o" /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-seq.so.12.0.0 libbpp-seq.so.12 libbpp-seq.so +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 92%] Built target bpp-seq-shared +make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/depend +make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/depend +make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend +make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/depend +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_alphabets.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_alignment_scores.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_containers.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +[ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 94%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 95%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +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: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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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_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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +[ 95%] Linking CXX executable test_containers +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' -[100%] Built target bpp-seq-static +[ 95%] Built target test_containers +make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/depend +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +[ 95%] Linking CXX executable test_alphabets +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 +[ 96%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 96%] Built target test_alphabets +make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend +make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +[ 97%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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%] Linking CXX executable test_bowker +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[ 98%] Linking CXX executable test_alignment_scores +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +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/test/test_io.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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, 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:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' + 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; + | ^~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 98%] Built target test_bowker +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-arm-linux-gnueabihf' +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_walker.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +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-arm-linux-gnueabihf' +[ 98%] Built target test_alignment_scores +[ 99%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 +[ 99%] Linking CXX executable test_sequences +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 99%] Built target test_sequences +[ 99%] Linking CXX executable test_io +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[ 99%] Built target test_io +[100%] Linking CXX executable test_walker +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' +[100%] Built target test_walker make[2]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' dh_auto_test - cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 + cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j3 +/usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl @@ -3231,26 +3267,32 @@ 3: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_bowker 3: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 3: 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 -1/7 Test #1: test_alignment_scores ............ Passed 0.01 sec test 4 Start 4: test_containers 4: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_containers 4: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 4: Test timeout computed to be: 60000 -3: 2 0.919699 -2/7 Test #2: test_alphabets ................... Passed 0.01 sec +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 +1/7 Test #1: test_alignment_scores ............ Passed 0.02 sec +2/7 Test #2: test_alphabets ................... Passed 0.02 sec test 5 Start 5: test_io 5: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_io 5: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 5: Test timeout computed to be: 60000 +test 6 + Start 6: test_sequences + +6: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_sequences +6: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test +6: Test timeout computed to be: 60000 +3: 2 0.919699 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- @@ -3258,13 +3300,13 @@ 4: 30 4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU 4: GAAGGCGG-GUUUUGCGACCGACG--UUUU -3/7 Test #4: test_containers .................. Passed 0.01 sec -test 6 - Start 6: test_sequences +3/7 Test #4: test_containers .................. Passed 0.02 sec +test 7 + Start 7: test_walker -6: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_sequences -6: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test -6: Test timeout computed to be: 60000 +7: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_walker +7: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test +7: Test timeout computed to be: 60000 6: --- Strict match --- 6: ATTT: 0 6: TCG: 3 @@ -3275,13 +3317,6 @@ 6: CTCAT: 19 6: AAGCA: 16 4/7 Test #6: test_sequences ................... Passed 0.01 sec -test 7 - Start 7: test_walker - -7: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf/test/test_walker -7: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test -7: Test timeout computed to be: 60000 -5: example.fasta contains 100 sequences 7: 0 A 4 7: 1 U 5 7: 2 G 6 @@ -3389,25 +3424,26 @@ 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% -5/7 Test #7: test_walker ...................... Passed 0.02 sec +5/7 Test #7: test_walker ...................... Passed 0.03 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 0.06 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%0.008 0.0442 0.0958 0.505 -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%0.012 0.0546 0.0996 0.5012 -7/7 Test #3: test_bowker ...................... Passed 29.06 sec +6/7 Test #5: test_io .......................... Passed 0.11 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%0.0106 0.055 0.1062 0.5056 +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%0.0106 0.0488 0.0976 0.4952 +7/7 Test #3: test_bowker ...................... Passed 42.77 sec 100% tests passed, 0 tests failed out of 7 -Total Test time (real) = 29.07 sec +Total Test time (real) = 42.78 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/libbpp-seq-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/libbpp-seq-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -3425,139 +3461,139 @@ -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Site.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQualityTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotation.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Sequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/GeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/StandardGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SymbolList.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentReaderFormat.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Phylip.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Clustal.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceReaderFormat.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequenceStream.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Stockholm.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Fasta.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/GenBank.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceStream.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceFactory.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Mase.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentWriterFormat.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex2Format.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPoly.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOAlignment.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceWriterFormat.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/SequenceFileIndex.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusIoSequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractIAlignment.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/StreamSequenceIterator.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOSequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DistanceMatrix.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/App -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/App/SequenceApplicationTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceExceptions.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DNAToRNA.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceIterator.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteIterator.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSequence.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/NucleicAcidsReplication.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/StringSequenceTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQuality.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSite.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SymbolListTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Sequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceExceptions.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SymbolList.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Site.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEASup30Index.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChargeIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/BLOSUM50.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DistanceMatrix.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NumericAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNA.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/Alphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/IntegerAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNY.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabetState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/DNA.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/WordAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NumericAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetState.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/Alphabet.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSite.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Transliterator.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CodonSiteTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotationTools.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWalker.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequencePositionIterators.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceIterator.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/StandardGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/GeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQuality.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQualityTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/VectorSequenceContainer.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/AlignedSequenceContainer.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.h --- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerExceptions.h --- Installing: 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/build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerExceptions.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/OrderedSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/VectorSequenceContainer.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerIterator.h -- Installing: 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Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWalker.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotationTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/StringSequenceTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/NucleicAcidsReplication.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotation.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CodonSiteTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequencePositionIterators.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteIterator.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DNAToRNA.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Transliterator.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPoly.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/SequenceFileIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceReaderFormat.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Mase.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOSequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/StreamSequenceIterator.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceFactory.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Fasta.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Stockholm.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Phylip.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentWriterFormat.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceStream.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex2Format.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequenceStream.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusIoSequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentReaderFormat.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/GenBank.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Clustal.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOAlignment.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceWriterFormat.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractIAlignment.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-arm-linux-gnueabihf' @@ -3620,12 +3656,14 @@ 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/20348/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20348/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/6134 and its subdirectories -I: Current time: Mon Sep 9 00:40:13 -12 2024 -I: pbuilder-time-stamp: 1725885613 +I: removing directory /srv/workspace/pbuilder/20348 and its subdirectories +I: Current time: Tue Sep 10 02:50:06 +14 2024 +I: pbuilder-time-stamp: 1725886206