Diff of the two buildlogs: -- --- b1/build.log 2023-04-19 14:12:44.491232800 +0000 +++ b2/build.log 2023-04-19 14:29:48.209801195 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 19 01:13:54 -12 2023 -I: pbuilder-time-stamp: 1681910034 +I: Current time: Wed May 22 10:35:48 +14 2024 +I: pbuilder-time-stamp: 1716323748 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./shasta_0.11.1.orig.tar.gz] I: copying [./shasta_0.11.1-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Dec 11 23:17:17 2022 -12 +gpgv: Signature made Tue Dec 13 01:17:17 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -26,52 +26,84 @@ dpkg-source: info: unpacking shasta_0.11.1-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7154/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 22 10:35 /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/21233/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='7154' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=21233 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.fkGYHhof/pbuilderrc_D1gZ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fkGYHhof/b1 --logfile b1/build.log shasta_0.11.1-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fkGYHhof/pbuilderrc_E2wx --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fkGYHhof/b2 --logfile b2/build.log --extrapackages usrmerge shasta_0.11.1-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink16-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 16 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/7154/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 21 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -412,7 +444,7 @@ Get: 269 http://deb.debian.org/debian bookworm/main arm64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 270 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB] Get: 271 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB] -Fetched 140 MB in 10s (14.0 MB/s) +Fetched 140 MB in 3s (49.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -1531,8 +1563,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/shasta-0.11.1/ && 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 > ../shasta_0.11.1-1_source.changes +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/shasta-0.11.1/ && 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 > ../shasta_0.11.1-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.11.1-1 dpkg-buildpackage: info: source distribution unstable @@ -1547,7 +1588,7 @@ dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt binnengegaan dh_auto_configure -- -DBUILD_ID=0.11.1 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON @@ -1589,78 +1630,90 @@ -- Build files have been written to: /build/shasta-0.11.1/obj-aarch64-linux-gnu -make[1]: Leaving directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt verlaten debian/rules override_dh_auto_build -make[1]: Entering directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt binnengegaan dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 -make[2]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[2]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan /usr/bin/cmake -S/build/shasta-0.11.1 -B/build/shasta-0.11.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/shasta-0.11.1/obj-aarch64-linux-gnu/CMakeFiles /build/shasta-0.11.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[3]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[3]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan cd /build/shasta-0.11.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/shasta-0.11.1 /build/shasta-0.11.1/staticLibrary /build/shasta-0.11.1/obj-aarch64-linux-gnu /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan cd /build/shasta-0.11.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/shasta-0.11.1 /build/shasta-0.11.1/dynamicLibrary /build/shasta-0.11.1/obj-aarch64-linux-gnu /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' -[ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/shasta-0.11.1/src/Align4.cpp -[ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/shasta-0.11.1/src/Align4.cpp +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/shasta-0.11.1/src/Alignment.cpp +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/shasta-0.11.1/src/Alignment.cpp +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/shasta-0.11.1/src/AlignmentGraph.cpp +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerCompressedAssemblyGraph.cpp -[ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o +[ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/shasta-0.11.1/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp -[ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/shasta-0.11.1/src/Alignment.cpp -[ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o +[ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerAlignmentGraph.cpp +[ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/shasta-0.11.1/src/AssemblerDetangle.cpp -[ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/shasta-0.11.1/src/AlignmentGraph.cpp -[ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o +[ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-Alignments.cpp -[ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o +[ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-AssemblyGraph.cpp -[ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp -[ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/shasta-0.11.1/src/AssembledSegment.cpp In file included from /usr/include/c++/12/bits/exception_ptr.h:43, from /usr/include/c++/12/exception:168, from /usr/include/c++/12/ios:39, @@ -1718,6 +1771,8 @@ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ +[ 15%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/shasta-0.11.1/src/AssemblerAlignments.cpp In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, @@ -1758,59 +1813,173 @@ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -[ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o +[ 16%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp +[ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-MarkerGraph.cpp -[ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /build/shasta-0.11.1/src/Assembler.cpp -[ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o +[ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-Mode3.cpp -[ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o +[ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-ReadGraph.cpp -[ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-Reads.cpp In file included from /build/shasta-0.11.1/src/AssemblerHttpServer-MarkerGraph.cpp:7: /build/shasta-0.11.1/src/hsv.hpp: In function ‘std::pair shasta::hsvToHsl(double, double)’: /build/shasta-0.11.1/src/hsv.hpp:16:70: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 16 | inline std::pair shasta::hsvToHsl(double SV, double V) | ^ -[ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o +[ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerCompressedAssemblyGraph.cpp +[ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-Reads.cpp +[ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/shasta-0.11.1/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp +In file included from /usr/include/c++/12/bits/exception_ptr.h:43, + from /usr/include/c++/12/exception:168, + from /usr/include/c++/12/ios:39, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/shasta-0.11.1/src/iostream.hpp:4, + from /build/shasta-0.11.1/src/ReadId.hpp:11, + from /build/shasta-0.11.1/src/OrientedReadPair.hpp:5, + from /build/shasta-0.11.1/src/Alignment.hpp:4, + from /build/shasta-0.11.1/src/Assembler.hpp:5, + from /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:2: +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, + inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, + inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, + inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1203:29: +/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] + 206 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, + from /usr/include/c++/12/bits/allocator.h:46, + from /usr/include/c++/12/string:41, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42: +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, + inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, + inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, + inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, + inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, + inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1193:48: +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ + 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, + inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, + inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, + inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1224:33: +/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] + 206 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, + inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, + inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, + inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, + inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, + inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1214:53: +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ + 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, + inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, + inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, + inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1023:29: +/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] + 206 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, + inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, + inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, + inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, + inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, + inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1013:48: +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ + 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, + inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, + inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, + inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1043:33: +/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] + 206 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, + inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, + inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, + inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, + inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, + inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, + inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1033:53: +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ + 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ +[ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/shasta-0.11.1/src/AssemblerDetangle.cpp +[ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer.cpp -[ 16%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o +[ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -c /build/shasta-0.11.1/src/AssemblerHttpServer-Mode3.cpp +[ 28%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerReadGraph.cpp -[ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o +[ 29%] Building CXX object 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o +[ 37%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -c /build/shasta-0.11.1/src/Histogram.cpp -[ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o +[ 38%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -c /build/shasta-0.11.1/src/HttpServer.cpp -[ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o +[ 38%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o cd 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/build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/shasta-0.11.1/src/LocalAlignmentCandidateGraph.cpp -[ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o +[ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/shasta-0.11.1/src/LocalAlignmentGraph.cpp -[ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/shasta-0.11.1/src/AssemblerAlignmentCandidates.cpp -[ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerAlignmentGraph.cpp +[ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/LocalAssemblyGraph.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, @@ -1878,6 +2057,8 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/shasta-0.11.1/src/AssemblerLowHash.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, @@ -1899,12 +2080,10 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [17, 9223372036854775807] and 17 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/shasta-0.11.1/src/AssemblerAlignments.cpp -[ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/LocalAssemblyGraph.cpp -[ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /build/shasta-0.11.1/src/AssemblerAnalyzePaths.cpp +[ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerMarkerConnectivityGraph.cpp +[ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph-Write.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -1927,8 +2106,6 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -1940,8 +2117,8 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/shasta-0.11.1/src/AssemblerAssemblyGraph2.cpp +[ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerMarkerGraph.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -1953,224 +2130,137 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph-Write.cpp -[ 34%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o +[ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/shasta-0.11.1/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp +[ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph.cpp -[ 34%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o +[ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/shasta-0.11.1/src/LocalReadGraph.cpp -[ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblerCompressedAssemblyGraph.cpp -[ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o +[ 43%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/shasta-0.11.1/src/LongBaseSequence.cpp -In file included from /usr/include/c++/12/bits/exception_ptr.h:43, - from /usr/include/c++/12/exception:168, - from /usr/include/c++/12/ios:39, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/shasta-0.11.1/src/iostream.hpp:4, - from /build/shasta-0.11.1/src/ReadId.hpp:11, - from /build/shasta-0.11.1/src/OrientedReadPair.hpp:5, - from /build/shasta-0.11.1/src/Alignment.hpp:4, - from /build/shasta-0.11.1/src/Assembler.hpp:5, - from /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:2: -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, - inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, - inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, - inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1203:29: -/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] - 206 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, - from /usr/include/c++/12/bits/allocator.h:46, - from /usr/include/c++/12/string:41, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42: -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, - inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, - inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, - inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, - inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, - inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1193:48: -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ - 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, - inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, - inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, - inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1224:33: -/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] - 206 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, - inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, - inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, - inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, - inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, - inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1214:53: -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ - 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -[ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o +[ 43%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -c /build/shasta-0.11.1/src/LowHash0.cpp -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, - inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, - inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, - inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1023:29: -/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] - 206 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, - inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, - inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, - inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, - inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, - inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1013:48: -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ - 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algobase.h:182:11, - inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1107:18, - inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:1134:21, - inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1043:33: -/usr/include/c++/12/bits/move.h:206:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] - 206 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, - inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/allocator.h:188:40, - inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, - inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, - inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, - inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:552:47, - inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1033:53: -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ - 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -[ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/shasta-0.11.1/src/AssemblerOptions.cpp +[ 62%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -c /build/shasta-0.11.1/src/mode3.cpp -[ 59%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o +[ 63%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -c /build/shasta-0.11.1/src/performanceLog.cpp +[ 63%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /build/shasta-0.11.1/src/platformDependent.cpp +In file included from /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:2: +In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, + inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2431:68, + inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2465:72, + inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, + inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:22: +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t1’ is used uninitialized [-Wuninitialized] + 29 | class shasta::mode3::LocalAssemblyGraphVertex { + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here + 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); + | ^ +In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, + inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2431:68, + inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2465:72, + inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, + inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:22: +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t2’ is used uninitialized [-Wuninitialized] + 29 | class shasta::mode3::LocalAssemblyGraphVertex { + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: +/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here + 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); + | ^ +[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/shasta-0.11.1/src/runCommandWithTimeout.cpp In file included from /usr/include/c++/12/istream:39, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, @@ -2204,35 +2294,8 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ -[ 59%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /build/shasta-0.11.1/src/platformDependent.cpp -In file included from /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:2: -In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, - inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2431:68, - inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2465:72, - inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, - inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:22: -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t1’ is used uninitialized [-Wuninitialized] - 29 | class shasta::mode3::LocalAssemblyGraphVertex { - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here - 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); - | ^ -In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, - inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2431:68, - inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2465:72, - inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, - inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:22: -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t2’ is used uninitialized [-Wuninitialized] - 29 | class shasta::mode3::LocalAssemblyGraphVertex { - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: -/build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here - 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); - | ^ -[ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/shasta-0.11.1/src/runCommandWithTimeout.cpp +[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /build/shasta-0.11.1/src/shastaLapack.cpp In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2431:68, inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2465:72, @@ -2285,44 +2348,26 @@ /build/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); | ^ -[ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /build/shasta-0.11.1/src/shastaLapack.cpp -[ 61%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o +[ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /build/shasta-0.11.1/src/testSpoa.cpp -[ 61%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o +[ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/shasta-0.11.1/src/testSubsetGraph.cpp -[ 62%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /build/shasta-0.11.1/src/timestamp.cpp -[ 62%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/shasta-0.11.1/src/AssemblyGraph2.cpp +[ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblyPathGraph.cpp In file included from /build/shasta-0.11.1/src/ReadId.hpp:5, from /build/shasta-0.11.1/src/OrientedReadPair.hpp:5, from /build/shasta-0.11.1/src/Alignment.hpp:4, @@ -2339,10 +2384,6 @@ /build/shasta-0.11.1/src/AssemblerReadGraph.cpp:2053:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2053 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/shasta-0.11.1/src/AssemblyPathGraph.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/shasta-0.11.1/src/AssemblyPathGraph2.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o @@ -2355,31 +2396,22 @@ cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -c /build/shasta-0.11.1/src/ConfigurationTable.cpp [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -c /build/shasta-0.11.1/src/ConsensusCaller.cpp -[ 73%] Linking CXX static library shasta.a -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 -/usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o 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"CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -/usr/bin/ranlib shasta.a -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' -[ 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-ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/shasta-0.11.1/src/LocalAssemblyGraph.cpp -[ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o +[ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph-Write.cpp -[ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, @@ -2420,8 +2452,6 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/shasta-0.11.1/src/LocalReadGraph.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2433,6 +2463,8 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/shasta-0.11.1/src/LocalMarkerGraph.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2466,6 +2498,15 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o 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78%] Built target shastaStaticLibrary [ 78%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/shasta-0.11.1/src/LongBaseSequence.cpp [ 78%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o @@ -2502,14 +2543,14 @@ cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o -c /build/shasta-0.11.1/src/Reads.cpp [ 86%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /build/shasta-0.11.1/src/ReferenceOverlapMap.cpp -[ 86%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/shasta-0.11.1/src/SHASTA_ASSERT.cpp -[ 87%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/shasta-0.11.1/src/ShortBaseSequence.cpp /build/shasta-0.11.1/src/PhasingGraph.cpp: In member function ‘void shasta::PhasingGraphEdge::runBayesianModel(double, bool)’: /build/shasta-0.11.1/src/PhasingGraph.cpp:26:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 26 | tie(logPin, logPout) = diploidBayesianPhase(matrix, epsilon); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/shasta-0.11.1/src/SHASTA_ASSERT.cpp +[ 87%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/shasta-0.11.1/src/ShortBaseSequence.cpp [ 87%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -c /build/shasta-0.11.1/src/SimpleBayesianConsensusCaller-Builtin.cpp [ 88%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o @@ -2526,14 +2567,14 @@ cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o -c /build/shasta-0.11.1/src/computeRunLengthRepresentation.cpp [ 91%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o -c /build/shasta-0.11.1/src/diploidBayesianPhase.cpp -[ 91%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -c /build/shasta-0.11.1/src/dset64Test.cpp -[ 92%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -c /build/shasta-0.11.1/src/extractKmer.cpp /build/shasta-0.11.1/src/diploidBayesianPhase.cpp: In function ‘std::pair shasta::diploidBayesianPhase(const std::array, 2>&, double)’: /build/shasta-0.11.1/src/diploidBayesianPhase.cpp:27:19: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 27 | double epsilon) | ^ +[ 91%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -c /build/shasta-0.11.1/src/dset64Test.cpp +[ 92%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -c /build/shasta-0.11.1/src/extractKmer.cpp [ 92%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -c /build/shasta-0.11.1/src/filesystem.cpp [ 92%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o @@ -2562,8 +2603,6 @@ cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -c /build/shasta-0.11.1/src/shastaLapack.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -c /build/shasta-0.11.1/src/testSpoa.cpp -[ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/shasta-0.11.1/src/testSubsetGraph.cpp In file included from /usr/include/c++/12/istream:39, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, @@ -2597,6 +2636,8 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ +[ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o +cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/shasta-0.11.1/src/testSubsetGraph.cpp [ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -c /build/shasta-0.11.1/src/timestamp.cpp [100%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o @@ -2604,27 +2645,27 @@ [100%] Linking CXX shared library shasta.so cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o 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CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lpthread -lz -lspoa -llapack -lblas -lpython3.11 -ldl -lm -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten [100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan cd /build/shasta-0.11.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/shasta-0.11.1 /build/shasta-0.11.1/dynamicExecutable /build/shasta-0.11.1/obj-aarch64-linux-gnu /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicExecutable /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build -make[4]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan [100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/shasta-0.11.1/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -g0 -O3 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/shasta-0.11.1/srcMain/main.cpp [100%] Linking CXX executable shastaDynamic cd /build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/shasta-0.11.1/obj-aarch64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lspoa -lpng -lz -llapack -lblas -lgfortran -lpthread -lpython3.11 -ldl -lm -make[4]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[4]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten [100%] Built target shastaDynamicExecutable -make[3]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[3]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten /usr/bin/cmake -E cmake_progress_start /build/shasta-0.11.1/obj-aarch64-linux-gnu/CMakeFiles 0 -make[2]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[2]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; -cp: './docs/PythonApi/shasta.so' and 'docs/PythonApi/shasta.so' are the same file +cp: './docs/PythonApi/shasta.so' en 'docs/PythonApi/shasta.so' zijn hetzelfde bestand PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v5.3.0 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). @@ -2650,18 +2691,18 @@ build succeeded, 2 warnings. The HTML pages are in build/html. -make[1]: Leaving directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt verlaten dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/shasta-0.11.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[1]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan /usr/bin/cmake -S/build/shasta-0.11.1 -B/build/shasta-0.11.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall -make[2]: Entering directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' -make[2]: Nothing to be done for 'preinstall'. -make[2]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[2]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt binnengegaan +make[2]: Er hoeft niets gedaan te worden voor 'preinstall'. +make[2]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" @@ -2896,9 +2937,9 @@ -- Installing: /build/shasta-0.11.1/debian/tmp/build/shasta-0.11.1/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /build/shasta-0.11.1/debian/tmp/build/shasta-0.11.1/obj-aarch64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /build/shasta-0.11.1/debian/tmp/build/shasta-0.11.1/obj-aarch64-linux-gnu/./shasta-install/docs/Acknowledgments.html -make[1]: Leaving directory '/build/shasta-0.11.1/obj-aarch64-linux-gnu' +make[1]: Map '/build/shasta-0.11.1/obj-aarch64-linux-gnu' wordt verlaten debian/rules override_dh_install-arch -make[1]: Entering directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt binnengegaan dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta @@ -2911,7 +2952,7 @@ patchelf \ --replace-needed shasta.so shasta.cpython-311-aarch64-linux-gnu.so \ debian/shasta/usr/bin/shasta -make[1]: Leaving directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt verlaten dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc @@ -2921,11 +2962,11 @@ dh_python3 I: dh_python3 fs:483: renaming shasta.so to shasta.cpython-311-aarch64-linux-gnu.so debian/rules execute_after_dh_python3-arch -make[1]: Entering directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt binnengegaan patchelf \ --set-soname shasta.cpython-311-aarch64-linux-gnu.so \ /build/shasta-0.11.1/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-aarch64-linux-gnu.so -make[1]: Leaving directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt verlaten dh_lintian dh_perl dh_link @@ -2933,7 +2974,7 @@ dh_compress dh_fixperms debian/rules override_dh_missing -make[1]: Entering directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt binnengegaan # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed @@ -2946,7 +2987,7 @@ # Remove rest of files which have already been installed rm -rf debian/tmp//build/shasta-0.11.1 dh_missing --list-missing -make[1]: Leaving directory '/build/shasta-0.11.1' +make[1]: Map '/build/shasta-0.11.1' wordt verlaten dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-aarch64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present @@ -2957,11 +2998,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'shasta' in '../shasta_0.11.1-1_arm64.deb'. -dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.11.1-1_arm64.deb'. -dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.11.1-1_arm64.deb'. -dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.11.1-1_all.deb'. -dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.11.1-1_arm64.deb'. +dpkg-deb: pakket 'shasta' wordt gebouwd in '../shasta_0.11.1-1_arm64.deb'. +dpkg-deb: pakket 'shasta-dbgsym' wordt gebouwd in '../shasta-dbgsym_0.11.1-1_arm64.deb'. +dpkg-deb: pakket 'python3-shasta' wordt gebouwd in '../python3-shasta_0.11.1-1_arm64.deb'. +dpkg-deb: pakket 'python3-shasta-dbgsym' wordt gebouwd in '../python3-shasta-dbgsym_0.11.1-1_arm64.deb'. +dpkg-deb: pakket 'python3-shasta-doc' wordt gebouwd in '../python3-shasta-doc_0.11.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.11.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.11.1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2969,12 +3010,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/21233/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21233/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/7154 and its subdirectories -I: Current time: Wed Apr 19 02:12:43 -12 2023 -I: pbuilder-time-stamp: 1681913563 +I: removing directory /srv/workspace/pbuilder/21233 and its subdirectories +I: Current time: Wed May 22 10:52:47 +14 2024 +I: pbuilder-time-stamp: 1716324767