Tue Sep 30 03:58:48 UTC 2025 I: starting to build shasta/forky/arm64 on jenkins on '2025-09-30 03:58' Tue Sep 30 03:58:48 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/100690/console.log Tue Sep 30 03:58:48 UTC 2025 I: Downloading source for forky/shasta=0.12.0-1 --2025-09-30 03:58:48-- http://deb.debian.org/debian/pool/main/s/shasta/shasta_0.12.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2556 (2.5K) [text/prs.lines.tag] Saving to: ‘shasta_0.12.0-1.dsc’ 0K .. 100% 292M=0s 2025-09-30 03:58:48 (292 MB/s) - ‘shasta_0.12.0-1.dsc’ saved [2556/2556] Tue Sep 30 03:58:48 UTC 2025 I: shasta_0.12.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shasta Binary: shasta, python3-shasta, python3-shasta-doc Architecture: any-amd64 arm64 all Version: 0.12.0-1 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust , Étienne Mollier Homepage: https://github.com/chanzuckerberg/shasta Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/shasta Vcs-Git: https://salsa.debian.org/med-team/shasta.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev [any-amd64], libcereal-dev, libblas-dev, liblapack-dev, gfortran Package-List: python3-shasta deb python optional arch=any-amd64,arm64 python3-shasta-doc deb doc optional arch=all shasta deb science optional arch=any-amd64,arm64 Checksums-Sha1: 468ada59ae9bce71bf11ff0a2e109fa1ad9977e7 9602137 shasta_0.12.0.orig.tar.gz 211503e8daf13ec3a1e1f5e1a56d4e9f03355247 10120 shasta_0.12.0-1.debian.tar.xz Checksums-Sha256: 39a7fcc49df93d903d8a1ed21a57a7533fc44897cb58194bfd089356f36cfdc9 9602137 shasta_0.12.0.orig.tar.gz 2ed0b0cd1b6ac9960b92a3b26e7ab1be5e58c13fe65c4fdb20a75caeb2d07333 10120 shasta_0.12.0-1.debian.tar.xz Files: 6f61f2536ecadcb827b822af5d22f8a6 9602137 shasta_0.12.0.orig.tar.gz 52c1981c540bf79fc17ca6b60885c04c 10120 shasta_0.12.0-1.debian.tar.xz Dgit: 77c67b611fa7811c48fd7ca1fafff3a53b31a816 debian archive/debian/0.12.0-1 https://git.dgit.debian.org/shasta -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZTYYYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpdfg//XE2eew/aF0eEanRKG15kz1g+SheC /YAtH1XbXtQpH7FX1MDhWHP5K7n68DqsXG7Gyw0arZAthezEYn/xyZXxBh09sgwm x4k9F8e5u2lDWlqcIhqTh4j2VsdVG6/dGBEqnDdgvlQ9YIIGHdMlmrgQ3glHQjVS BhcaVMdTPXfV9lo1w3WFxYjU/sEC0OEvuGQX49Uu5oE0nu7tAHAno6es1zelaXHI 8AHRPlDVTCZhMPV4TDljAmjvpEbAWK/HsqVaamoqpwTPcJbpgI/XrGIVp2Ws/y+b BTWmJNHWvS1u8DojftcOjrywuVckMkVUqoYbEzUq5QUYhLJaso+Nzq4BE9BHzdne LCfJXuvISxcSkNX+3eMJWwOiUz6CMR/LyI2iXRvZkbkUWoJT0Hr+rp0CWnnzBgKF LAJEtAi+K+3koZAXM53rKrblcKsroXuKwSrOvuqqcv5CwJetvN2Wg1ZCAqP1vshb IobvMeSUX1O7++Qp6xYYbhKn6uwLjMpY4mm5xkjum/U4WQ52iOnCIQOLD3n+bNze 5+XKpaktXooPx2a685JTvl4pzQjajt8Y1bdyVuVSRbuLpbiE3886jb9Bx1Rcg6rC hQRFQOw352bmpI8fvCi81NEsR3Jm0yrGcVo/ZJz56rMeZMQLvUvG+eHHcXzh44MG 9l5k8BdLVrmpRfY= =ys3d -----END PGP SIGNATURE----- Tue Sep 30 03:58:48 UTC 2025 I: Checking whether the package is not for us Tue Sep 30 03:58:48 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Sep 30 03:58:48 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Sep 30 04:06:11 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 1 22:21:50 -12 2026 I: pbuilder-time-stamp: 1793614910 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shasta_0.12.0-1.dsc] I: copying [./shasta_0.12.0.orig.tar.gz] I: copying [./shasta_0.12.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./shasta_0.12.0-1.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.12.0 dpkg-source: info: unpacking shasta_0.12.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/934991/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='fdd14276c1594e61b57ecbcaf2dd7b90' 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='934991' PS1='# ' PS2='> ' 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.9zSIZHr1/pbuilderrc_jgZB --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/934991/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcereal-dev, libblas-dev, liblapack-dev, gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20001 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on patchelf; however: Package patchelf is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} gfortran{a} gfortran-15{a} gfortran-15-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcereal-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgfortran-15-dev{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu76{a} libidn2-0{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmunge2{a} libncbi-vdb3{a} libnghttp2-14{a} libnghttp3-9{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libstdc++-14-dev{a} libtasn1-6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchelf{a} po-debconf{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-roman-numerals{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libpng-tools libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 302 newly installed, 0 to remove and 0 not upgraded. Need to get 282 MB of archives. After unpacking 1516 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.7-1 [857 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.7-1 [2001 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.7-1 [1895 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 openssl arm64 3.5.3-1 [1457 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 ca-certificates all 20250419 [162 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libfido2-1 arm64 1.16.0-2 [74.4 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 36 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 openssh-client arm64 1:10.0p1-8 [925 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.11.0-1 [66.7 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-1 [388 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 67 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.27 [92.2 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 73 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 debhelper all 13.27 [940 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 gcc-14-base arm64 14.3.0-8 [52.1 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-4 [371 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libgfortran-15-dev arm64 15.2.0-4 [411 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-4 [76.9 MB] Get: 88 http://deb.debian.org/debian forky/main arm64 gfortran-15 arm64 15.2.0-4 [17.9 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4 [1280 B] Get: 90 http://deb.debian.org/debian forky/main arm64 gfortran arm64 4:15.2.0-4 [1428 B] Get: 91 http://deb.debian.org/debian forky/main arm64 libnl-3-200 arm64 3.11.0-2 [57.9 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libnl-route-3-200 arm64 3.11.0-2 [176 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libibverbs1 arm64 56.1-1+b1 [59.8 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 ibverbs-providers arm64 56.1-1+b1 [338 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 icu-devtools arm64 76.1-4 [200 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libllvm17t64 arm64 1:17.0.6-22+b3 [21.3 MB] Get: 99 http://deb.debian.org/debian forky/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 100 http://deb.debian.org/debian forky/main arm64 libdrm-common all 2.4.125-2 [8576 B] Get: 101 http://deb.debian.org/debian forky/main arm64 libdrm2 arm64 2.4.125-2 [38.4 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libdrm-amdgpu1 arm64 2.4.125-2 [22.3 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libhsakmt1 arm64 6.2.4+ds-1 [58.3 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libhsa-runtime64-1 arm64 6.1.2-3 [302 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libamdhip64-5 arm64 5.7.1-6 [8824 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libblas-dev arm64 3.12.1-7 [145 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgcc-14-dev arm64 14.3.0-8 [2364 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libstdc++-14-dev arm64 14.3.0-8 [2567 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libboost1.83-dev arm64 1.83.0-5 [10.6 MB] Get: 112 http://deb.debian.org/debian forky/main arm64 libboost-atomic1.83.0 arm64 1.83.0-5 [234 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libboost-atomic1.83-dev arm64 1.83.0-5 [235 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libboost-atomic-dev arm64 1.83.0.2+b2 [3892 B] Get: 115 http://deb.debian.org/debian forky/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-5 [240 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 libboost-chrono1.83-dev arm64 1.83.0-5 [245 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libboost-chrono-dev arm64 1.83.0.2+b2 [4212 B] Get: 118 http://deb.debian.org/debian forky/main arm64 libboost-container1.83.0 arm64 1.83.0-5 [259 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libboost-container1.83-dev arm64 1.83.0-5 [265 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libboost-container-dev arm64 1.83.0.2+b2 [4064 B] Get: 121 http://deb.debian.org/debian forky/main arm64 libboost-date-time1.83.0 arm64 1.83.0-5 [231 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libboost-serialization1.83.0 arm64 1.83.0-5 [325 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libboost-serialization1.83-dev arm64 1.83.0-5 [374 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libboost-date-time1.83-dev arm64 1.83.0-5 [239 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 libboost-system1.83.0 arm64 1.83.0-5 [231 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 libboost-system1.83-dev arm64 1.83.0-5 [232 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libboost-thread1.83.0 arm64 1.83.0-5 [266 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libboost-thread1.83-dev arm64 1.83.0-5 [277 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 libboost-context1.83.0 arm64 1.83.0-5 [232 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 libboost-context1.83-dev arm64 1.83.0-5 [233 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 libboost-context-dev arm64 1.83.0.2+b2 [3792 B] Get: 132 http://deb.debian.org/debian forky/main arm64 libboost-coroutine1.83.0 arm64 1.83.0-5 [235 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 libboost-coroutine1.83-dev arm64 1.83.0-5 [237 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 libboost-coroutine-dev arm64 1.83.0.2+b2 [3860 B] Get: 135 http://deb.debian.org/debian forky/main arm64 libboost-date-time-dev arm64 1.83.0.2+b2 [3584 B] Get: 136 http://deb.debian.org/debian forky/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 137 http://deb.debian.org/debian forky/main arm64 libboost-exception1.83-dev arm64 1.83.0-5 [230 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 libboost-exception-dev arm64 1.83.0.2+b2 [3572 B] Get: 139 http://deb.debian.org/debian forky/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-5 [273 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-5 [293 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 libboost-fiber1.83.0 arm64 1.83.0-5 [253 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 libboost-fiber1.83-dev arm64 1.83.0-5 [265 kB] Get: 143 http://deb.debian.org/debian forky/main arm64 libboost-fiber-dev arm64 1.83.0.2+b2 [4016 B] Get: 144 http://deb.debian.org/debian forky/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B] Get: 145 http://deb.debian.org/debian forky/main arm64 libboost-graph1.83.0 arm64 1.83.0-5 [342 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83.0 arm64 1.83.0-5 [314 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 libicu-dev arm64 76.1-4 [10.6 MB] Get: 148 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83-dev arm64 1.83.0-5 [335 kB] Get: 149 http://deb.debian.org/debian forky/main arm64 libboost-test1.83.0 arm64 1.83.0-5 [438 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 libboost-test1.83-dev arm64 1.83.0-5 [527 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 libboost-graph1.83-dev arm64 1.83.0-5 [373 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B] Get: 153 http://deb.debian.org/debian forky/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 librdmacm1t64 arm64 56.1-1+b1 [67.9 kB] Get: 156 http://deb.debian.org/debian forky/main arm64 libfabric1 arm64 2.1.0-1.1 [548 kB] Get: 157 http://deb.debian.org/debian forky/main arm64 libhwloc15 arm64 2.12.2-1 [142 kB] Get: 158 http://deb.debian.org/debian forky/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 159 http://deb.debian.org/debian forky/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 160 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 161 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 162 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 163 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 164 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 165 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 166 http://deb.debian.org/debian forky/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.7 kB] Get: 168 http://deb.debian.org/debian forky/main arm64 libhwloc-plugins arm64 2.12.2-1 [18.1 kB] Get: 169 http://deb.debian.org/debian forky/main arm64 libpmix2t64 arm64 6.0.0+really5.0.8-1 [574 kB] Get: 170 http://deb.debian.org/debian forky/main arm64 libibumad3 arm64 56.1-1+b1 [29.3 kB] Get: 171 http://deb.debian.org/debian forky/main arm64 libibmad5 arm64 56.1-1+b1 [42.8 kB] Get: 172 http://deb.debian.org/debian forky/main arm64 libucx0 arm64 1.19.0+ds-1 [1081 kB] Get: 173 http://deb.debian.org/debian forky/main arm64 libopenmpi40 arm64 5.0.8-10+b1 [2104 kB] Get: 174 http://deb.debian.org/debian forky/main arm64 libboost-mpi1.83.0 arm64 1.83.0-5 [268 kB] Get: 175 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel1.83.0 arm64 1.83.0-5 [276 kB] Get: 176 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel1.83-dev arm64 1.83.0-5 [284 kB] Get: 177 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel-dev arm64 1.83.0.2+b2 [3716 B] Get: 178 http://deb.debian.org/debian forky/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-5 [261 kB] Get: 179 http://deb.debian.org/debian forky/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 180 http://deb.debian.org/debian forky/main arm64 libboost-json1.83.0 arm64 1.83.0-5 [348 kB] Get: 181 http://deb.debian.org/debian forky/main arm64 libboost-json1.83-dev arm64 1.83.0-5 [372 kB] Get: 182 http://deb.debian.org/debian forky/main arm64 libboost-json-dev arm64 1.83.0.2+b2 [3696 B] Get: 183 http://deb.debian.org/debian forky/main arm64 libboost-locale1.83.0 arm64 1.83.0-5 [441 kB] Get: 184 http://deb.debian.org/debian forky/main arm64 libboost-locale1.83-dev arm64 1.83.0-5 [543 kB] Get: 185 http://deb.debian.org/debian forky/main arm64 libboost-locale-dev arm64 1.83.0.2+b2 [3916 B] Get: 186 http://deb.debian.org/debian forky/main arm64 libboost-log1.83.0 arm64 1.83.0-5 [644 kB] Get: 187 http://deb.debian.org/debian forky/main arm64 libboost-log1.83-dev arm64 1.83.0-5 [850 kB] Get: 188 http://deb.debian.org/debian forky/main arm64 libboost-log-dev arm64 1.83.0.2+b2 [3788 B] Get: 189 http://deb.debian.org/debian forky/main arm64 libboost-math1.83.0 arm64 1.83.0-5 [471 kB] Get: 190 http://deb.debian.org/debian forky/main arm64 libboost-math1.83-dev arm64 1.83.0-5 [536 kB] Get: 191 http://deb.debian.org/debian forky/main arm64 libboost-math-dev arm64 1.83.0.2+b2 [3784 B] Get: 192 http://deb.debian.org/debian forky/main arm64 openmpi-common all 5.0.8-10 [97.5 kB] Get: 193 http://deb.debian.org/debian forky/main arm64 libnl-3-dev arm64 3.11.0-2 [104 kB] Get: 194 http://deb.debian.org/debian forky/main arm64 libnl-route-3-dev arm64 3.11.0-2 [210 kB] Get: 195 http://deb.debian.org/debian forky/main arm64 libibverbs-dev arm64 56.1-1+b1 [649 kB] Get: 196 http://deb.debian.org/debian forky/main arm64 libnuma-dev arm64 2.0.19-1 [37.6 kB] Get: 197 http://deb.debian.org/debian forky/main arm64 libltdl7 arm64 2.5.4-5 [415 kB] Get: 198 http://deb.debian.org/debian forky/main arm64 libltdl-dev arm64 2.5.4-5 [168 kB] Get: 199 http://deb.debian.org/debian forky/main arm64 libhwloc-dev arm64 2.12.2-1 [239 kB] Get: 200 http://deb.debian.org/debian forky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 201 http://deb.debian.org/debian forky/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 202 http://deb.debian.org/debian forky/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 203 http://deb.debian.org/debian forky/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 204 http://deb.debian.org/debian forky/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 205 http://deb.debian.org/debian forky/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 206 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 207 http://deb.debian.org/debian forky/main arm64 openmpi-bin arm64 5.0.8-10+b1 [184 kB] Get: 208 http://deb.debian.org/debian forky/main arm64 libopenmpi-dev arm64 5.0.8-10+b1 [1090 kB] Get: 209 http://deb.debian.org/debian forky/main arm64 mpi-default-dev arm64 1.19 [3432 B] Get: 210 http://deb.debian.org/debian forky/main arm64 libboost-mpi1.83-dev arm64 1.83.0-5 [291 kB] Get: 211 http://deb.debian.org/debian forky/main arm64 libboost-mpi-dev arm64 1.83.0.2+b2 [3668 B] Get: 212 http://deb.debian.org/debian forky/main arm64 libboost-python1.83.0 arm64 1.83.0-5 [296 kB] Get: 213 http://deb.debian.org/debian forky/main arm64 mpi-default-bin arm64 1.19 [2640 B] Get: 214 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python1.83.0 arm64 1.83.0-5 [343 kB] Get: 215 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python1.83-dev arm64 1.83.0-5 [237 kB] Get: 216 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python-dev arm64 1.83.0.2+b2 [3700 B] Get: 217 http://deb.debian.org/debian forky/main arm64 libboost-nowide1.83.0 arm64 1.83.0-5 [234 kB] Get: 218 http://deb.debian.org/debian forky/main arm64 libboost-nowide1.83-dev arm64 1.83.0-5 [236 kB] Get: 219 http://deb.debian.org/debian forky/main arm64 libboost-nowide-dev arm64 1.83.0.2+b2 [3660 B] Get: 220 http://deb.debian.org/debian forky/main arm64 libboost-numpy1.83.0 arm64 1.83.0-5 [241 kB] Get: 221 http://deb.debian.org/debian forky/main arm64 libboost-numpy1.83-dev arm64 1.83.0-5 [246 kB] Get: 222 http://deb.debian.org/debian forky/main arm64 libboost-numpy-dev arm64 1.83.0.2+b2 [3632 B] Get: 223 http://deb.debian.org/debian forky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-5 [331 kB] Get: 224 http://deb.debian.org/debian forky/main arm64 libboost-program-options1.83-dev arm64 1.83.0-5 [369 kB] Get: 225 http://deb.debian.org/debian forky/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 226 http://deb.debian.org/debian forky/main arm64 libpython3.13 arm64 3.13.7-1 [1978 kB] Get: 227 http://deb.debian.org/debian forky/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 228 http://deb.debian.org/debian forky/main arm64 libpython3.13-dev arm64 3.13.7-1 [4924 kB] Get: 229 http://deb.debian.org/debian forky/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 230 http://deb.debian.org/debian forky/main arm64 python3.13-dev arm64 3.13.7-1 [504 kB] Get: 231 http://deb.debian.org/debian forky/main arm64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 232 http://deb.debian.org/debian forky/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 233 http://deb.debian.org/debian forky/main arm64 libboost-python1.83-dev arm64 1.83.0-5 [322 kB] Get: 234 http://deb.debian.org/debian forky/main arm64 libboost-python-dev arm64 1.83.0.2+b2 [3880 B] Get: 235 http://deb.debian.org/debian forky/main arm64 libboost-random1.83.0 arm64 1.83.0-5 [238 kB] Get: 236 http://deb.debian.org/debian forky/main arm64 libboost-random1.83-dev arm64 1.83.0-5 [241 kB] Get: 237 http://deb.debian.org/debian forky/main arm64 libboost-random-dev arm64 1.83.0.2+b2 [3584 B] Get: 238 http://deb.debian.org/debian forky/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 239 http://deb.debian.org/debian forky/main arm64 libboost-serialization-dev arm64 1.83.0.2+b2 [3816 B] Get: 240 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace1.83.0 arm64 1.83.0-5 [277 kB] Get: 241 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace1.83-dev arm64 1.83.0-5 [245 kB] Get: 242 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace-dev arm64 1.83.0.2+b2 [3580 B] Get: 243 http://deb.debian.org/debian forky/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 244 http://deb.debian.org/debian forky/main arm64 libboost-test-dev arm64 1.83.0.2+b2 [3620 B] Get: 245 http://deb.debian.org/debian forky/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 246 http://deb.debian.org/debian forky/main arm64 libboost-timer1.83.0 arm64 1.83.0-5 [235 kB] Get: 247 http://deb.debian.org/debian forky/main arm64 libboost-timer1.83-dev arm64 1.83.0-5 [237 kB] Get: 248 http://deb.debian.org/debian forky/main arm64 libboost-timer-dev arm64 1.83.0.2+b2 [3712 B] Get: 249 http://deb.debian.org/debian forky/main arm64 libboost1.83-tools-dev arm64 1.83.0-5 [1408 kB] Get: 250 http://deb.debian.org/debian forky/main arm64 libboost-tools-dev arm64 1.83.0.2+b2 [3764 B] Get: 251 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure1.83.0 arm64 1.83.0-5 [245 kB] Get: 252 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure1.83-dev arm64 1.83.0-5 [250 kB] Get: 253 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure-dev arm64 1.83.0.2+b2 [3676 B] Get: 254 http://deb.debian.org/debian forky/main arm64 libboost-url1.83.0 arm64 1.83.0-5 [328 kB] Get: 255 http://deb.debian.org/debian forky/main arm64 libboost-url1.83-dev arm64 1.83.0-5 [423 kB] Get: 256 http://deb.debian.org/debian forky/main arm64 libboost-url-dev arm64 1.83.0.2+b2 [3720 B] Get: 257 http://deb.debian.org/debian forky/main arm64 libboost-wave1.83.0 arm64 1.83.0-5 [416 kB] Get: 258 http://deb.debian.org/debian forky/main arm64 libboost-wave1.83-dev arm64 1.83.0-5 [492 kB] Get: 259 http://deb.debian.org/debian forky/main arm64 libboost-wave-dev arm64 1.83.0.2+b2 [3616 B] Get: 260 http://deb.debian.org/debian forky/main arm64 libboost-all-dev arm64 1.83.0.2+b2 [3924 B] Get: 261 http://deb.debian.org/debian forky/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Get: 262 http://deb.debian.org/debian forky/main arm64 libcereal-dev arm64 1.3.2+dfsg-6 [221 kB] Get: 263 http://deb.debian.org/debian forky/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 264 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 265 http://deb.debian.org/debian forky/main arm64 liblapack-dev arm64 3.12.1-7 [3829 kB] Get: 266 http://deb.debian.org/debian forky/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 267 http://deb.debian.org/debian forky/main arm64 libmbedcrypto16 arm64 3.6.4-2 [346 kB] Get: 268 http://deb.debian.org/debian forky/main arm64 libmbedx509-7 arm64 3.6.4-2 [150 kB] Get: 269 http://deb.debian.org/debian forky/main arm64 libmbedtls21 arm64 3.6.4-2 [229 kB] Get: 270 http://deb.debian.org/debian forky/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 271 http://deb.debian.org/debian forky/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 272 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 273 http://deb.debian.org/debian forky/main arm64 libpng-dev arm64 1.6.50-1 [361 kB] Get: 274 http://deb.debian.org/debian forky/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 275 http://deb.debian.org/debian forky/main arm64 libspoa7.0.0 arm64 4.1.4-2+b1 [53.3 kB] Get: 276 http://deb.debian.org/debian forky/main arm64 libspoa-dev arm64 4.1.4-2+b1 [9788 B] Get: 277 http://deb.debian.org/debian forky/main arm64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 278 http://deb.debian.org/debian forky/main arm64 ncbi-blast+ arm64 2.16.0+ds-7 [14.5 MB] Get: 279 http://deb.debian.org/debian forky/main arm64 patchelf arm64 0.18.0-1.4 [89.3 kB] Get: 280 http://deb.debian.org/debian forky/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 281 http://deb.debian.org/debian forky/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 282 http://deb.debian.org/debian forky/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 283 http://deb.debian.org/debian forky/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 284 http://deb.debian.org/debian forky/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 285 http://deb.debian.org/debian forky/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 286 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.3-1 [123 kB] Get: 287 http://deb.debian.org/debian forky/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 288 http://deb.debian.org/debian forky/main arm64 python3-roman all 5.1-1 [11.0 kB] Get: 289 http://deb.debian.org/debian forky/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 290 http://deb.debian.org/debian forky/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 291 http://deb.debian.org/debian forky/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 292 http://deb.debian.org/debian forky/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 293 http://deb.debian.org/debian forky/main arm64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 294 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 295 http://deb.debian.org/debian forky/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 296 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 297 http://deb.debian.org/debian forky/main arm64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 298 http://deb.debian.org/debian forky/main arm64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 299 http://deb.debian.org/debian forky/main arm64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 300 http://deb.debian.org/debian forky/main arm64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 301 http://deb.debian.org/debian forky/main arm64 sphinx-common all 8.2.3-6 [619 kB] Get: 302 http://deb.debian.org/debian forky/main arm64 python3-sphinx all 8.2.3-6 [477 kB] Fetched 282 MB in 2s (159 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20001 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_arm64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:arm64 (3.13.7-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 20335 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.3-3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_arm64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (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 ... 21350 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-9_arm64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.5.3-1_arm64.deb ... Unpacking openssl (3.5.3-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.41.2-1_arm64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../013-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../015-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../016-libcbor0.10_0.10.2-2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../017-libfido2-1_1.16.0-2_arm64.deb ... Unpacking libfido2-1:arm64 (1.16.0-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../018-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:arm64. 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Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 2 10:22:50 UTC 2026. Universal Time is now: Mon Nov 2 10:22:50 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-5) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-5) ... Setting up libboost-numpy1.83.0 (1.83.0-5) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libmunge2:arm64 (0.5.16-1) ... Setting up libexpat1-dev:arm64 (2.7.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libboost-chrono1.83.0t64:arm64 (1.83.0-5) ... Setting up libjsoncpp26:arm64 (1.9.6-4) ... 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Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.11.0-2) ... Setting up libboost-graph1.83.0:arm64 (1.83.0-5) ... Setting up openmpi-common (5.0.8-10) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libboost-container1.83.0:arm64 (1.83.0-5) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libboost-type-erasure1.83.0:arm64 (1.83.0-5) ... Setting up cmake-data (4.1.1+really3.31.6-2) ... Setting up librhash1:arm64 (1.4.6-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libicu76:arm64 (76.1-4) ... Setting up libmbedcrypto16:arm64 (3.6.4-2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libboost-math1.83.0:arm64 (1.83.0-5) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libgcc-14-dev:arm64 (14.3.0-8) ... Setting up patchelf (0.18.0-1.4) ... Setting up libfido2-1:arm64 (1.16.0-2) ... Setting up openssl (3.5.3-1) ... Setting up libstdc++-14-dev:arm64 (14.3.0-8) ... Setting up libdrm-common (2.4.125-2) ... Setting up libarchive13t64:arm64 (3.7.4-4+b1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libboost1.83-tools-dev (1.83.0-5) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shasta-0.12.0/ && 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_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is aarch64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (1.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' 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/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/Align4.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Assembler.cpp [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Align4.cpp [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/Align4.cpp:15: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/Align4.cpp:15: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp:4: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Alignment.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp:7: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp:6: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Assembler.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp [ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp:25: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/c++/15/bits/exception_ptr.h:41, from /usr/include/c++/15/exception:168, from /usr/include/c++/15/ios:43, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1274:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46: 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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1264:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1295:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1285:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1094:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1084:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1114:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1104:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 16%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 17%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 623 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 18%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp:4: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp [ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp:10: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMode3.cpp [ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp:7: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp:6: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 26%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp:29: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 28%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp:25: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp In file included from /usr/include/c++/15/bits/exception_ptr.h:41, from /usr/include/c++/15/exception:168, from /usr/include/c++/15/ios:43, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1274:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46: 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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1264:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1295:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1285:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1094:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1084:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1114:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1104:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ConfigurationTable.cpp [ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 33%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ConsensusCaller.cpp [ 33%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Coverage.cpp [ 34%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/HashedKmerChecker.cpp [ 34%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 35%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/Histogram.cpp [ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/HttpServer.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 623 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/InducedAlignment.cpp [ 37%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerCheckerFactory.cpp [ 37%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 37%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::id’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::minMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API 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/build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp:10: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph1.cpp [ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong 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/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PeakFinder.cpp [ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PhasingGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ [ 50%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PngImage.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 50%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PythonModule.cpp [ 51%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReadGraph.cpp [ 51%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReadLoader.cpp [ 52%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Reads.cpp [ 52%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReferenceOverlapMap.cpp [ 52%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 52%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.cpp [ 53%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp [ 53%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 54%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 55%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ShortBaseSequence.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp:29: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 55%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 64%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp [ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/diploidBayesianPhase.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/dset64Test.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/enumeratePaths.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/extractKmer.cpp [ 66%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/filesystem.cpp [ 67%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/globalMsa.cpp [ 67%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/html.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.cpp [ 68%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/longestPath.cpp [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mappedCopy.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::id’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::minMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/markerAccessFunctions.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp [ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-AssemblyGraph.cpp [ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0.cpp [ 72%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasedComponent.cpp [ 72%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp:17: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PrimaryGraph.cpp [ 73%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph1.cpp [ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 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-Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/LocalReadGraph.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/LongBaseSequence.cpp [ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/platformDependent.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LowHash0.cpp [ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp [100%] Linking CXX static library shasta.a cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /build/reproducible-path/shasta-0.12.0/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 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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" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o 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/HashedKmerChecker.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/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.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/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.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/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/Mode3Assembler.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/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.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/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Built target shastaStaticLibrary [100%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/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/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/shastaDynamicLibrary.dir/link.d -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/AssemblerAlign5.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-MarkerGraph0.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.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/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 CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/s/usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libpng.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libboost_program_options.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libboost_serialization.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libspoa.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libpython3.13.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. hastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o 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/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.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 -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.13 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/srcMain/main.cpp [100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/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/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/shastaDynamicExecutable.dir/link.d CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lpthread -lpython3.13 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' # 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 PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v8.2.3 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/sidebar.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/classic.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: 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Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CreateAssemblyGraphVertices.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CreateCompressedAssemblyGraph.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CreateConfigurationTable.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CreateLocalSubgraph.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CreateMarkerGraphAndTransitiveReduction.py -- Installing: 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/build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerAlignment.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/MakeRelease.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Introduction.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/7.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/6.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/5.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/4.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/3.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/2.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/1.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Detangle-Before.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Detangle-After.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Configurations.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/ComputationalMethods.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Compatibility.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Commands.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/CommandLineOptions.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/ChooseMemoryOptions.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/CZI-new-logo.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/BuildingFromSource.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Acknowledgments.html make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:421: renaming shasta.so to shasta.cpython-313-aarch64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' patchelf \ --set-soname shasta.cpython-313-aarch64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/reproducible-path/shasta-0.12.0 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a dwz: dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so: .debug_info section not present debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-313-aarch64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_arm64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_arm64.deb'. dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_arm64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_arm64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/934991 and its subdirectories I: Current time: Sun Nov 1 22:29:07 -12 2026 I: pbuilder-time-stamp: 1793615347 Tue Sep 30 04:06:12 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Sep 30 04:06:12 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Sep 30 04:10:25 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Sep 30 04:10:25 UTC 2025 I: shasta_0.12.0-1_arm64.changes: Format: 1.8 Date: Sun, 26 May 2024 18:05:55 +0200 Source: shasta Binary: python3-shasta python3-shasta-dbgsym python3-shasta-doc shasta shasta-dbgsym Architecture: arm64 all Version: 0.12.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: python3-shasta - nanopore whole genome assembly (dynamic library) python3-shasta-doc - nanopore whole genome assembly (documentation) shasta - nanopore whole genome assembly (binaries and scripts) Changes: shasta (0.12.0-1) unstable; urgency=medium . * New upstream version 0.12.0 * gcc-13.patch: delete: applied upstream. * gcc-13-bis.patch: delete: applied upstream. * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 47fc4089b58989fbc60f8bf5eb16016ace6f72cb 138568 python3-shasta-dbgsym_0.12.0-1_arm64.deb 5c8617ad757e8540f61aa2b36d461c04faf0a280 23936 python3-shasta-doc_0.12.0-1_all.deb 91b05759a910e12175fd7e79fba56f5672104c8a 1947852 python3-shasta_0.12.0-1_arm64.deb 842418c140d3f339e5723a3d027e7b708c9369f3 9296 shasta-dbgsym_0.12.0-1_arm64.deb 43e340217ed0d139461bc061e1b3319d5a58d71d 15239 shasta_0.12.0-1_arm64.buildinfo 5a75369544a5a797c5f7aed9345eadd8ee6cf13c 618520 shasta_0.12.0-1_arm64.deb Checksums-Sha256: 5f33e9722cb36f806c0be92297a45708316ef2e411e7c79d7959fe5b0eef84f3 138568 python3-shasta-dbgsym_0.12.0-1_arm64.deb f236c5e320de1d8e961d6aae4bad9d009cfab171408eae6e8c4299181feb5e66 23936 python3-shasta-doc_0.12.0-1_all.deb 0232b62e29cabae69d47ee02cbb20012936d1976f5a00fb1204ac7ee5cfbb2fd 1947852 python3-shasta_0.12.0-1_arm64.deb f706ca67ac31b95c1b4139b211de5bc8cd0b2d184104ca8068ab172392f7e0e0 9296 shasta-dbgsym_0.12.0-1_arm64.deb 9a9dd0dfe8ec4b9c730ef2aa3fb7079d03aa6bd0b7c540adba32881d3be2a41b 15239 shasta_0.12.0-1_arm64.buildinfo 8774122b2a14046433df0ef7c4dd99f96df7a125de3a07b73426bfc303e48578 618520 shasta_0.12.0-1_arm64.deb Files: 66478d0ddb41deedcf1b753ca11d3c7a 138568 debug optional python3-shasta-dbgsym_0.12.0-1_arm64.deb 2b244f48052fe424a323639785c19718 23936 doc optional python3-shasta-doc_0.12.0-1_all.deb 930d553229845e97bc5af7403418e38f 1947852 python optional python3-shasta_0.12.0-1_arm64.deb ce58f62ac0a2776c17a48f5816653045 9296 debug optional shasta-dbgsym_0.12.0-1_arm64.deb 968af3bc791699d315a876066dbfd554 15239 science optional shasta_0.12.0-1_arm64.buildinfo 785b25087e85080494c4dcb57615f2c1 618520 science optional shasta_0.12.0-1_arm64.deb Tue Sep 30 04:10:25 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Sep 30 04:17:42 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 1 22:33:27 -12 2026 I: pbuilder-time-stamp: 1793615607 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shasta_0.12.0-1.dsc] I: copying [./shasta_0.12.0.orig.tar.gz] I: copying [./shasta_0.12.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./shasta_0.12.0-1.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.12.0 dpkg-source: info: unpacking shasta_0.12.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1060093/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e46f96f02d5547018f114c1edc4388fe' 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='1060093' PS1='# ' PS2='> ' 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.9zSIZHr1/pbuilderrc_TyDC --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1060093/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcereal-dev, libblas-dev, liblapack-dev, gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20000 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on patchelf; however: Package patchelf is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} gfortran{a} gfortran-15{a} gfortran-15-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcereal-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgfortran-15-dev{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu76{a} libidn2-0{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmunge2{a} libncbi-vdb3{a} libnghttp2-14{a} libnghttp3-9{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libstdc++-14-dev{a} libtasn1-6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchelf{a} po-debconf{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-roman-numerals{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libpng-tools libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 302 newly installed, 0 to remove and 0 not upgraded. Need to get 282 MB of archives. After unpacking 1516 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.7-1 [857 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.7-1 [2001 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.7-1 [1895 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 openssl arm64 3.5.3-1 [1457 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 ca-certificates all 20250419 [162 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libfido2-1 arm64 1.16.0-2 [74.4 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 36 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 openssh-client arm64 1:10.0p1-8 [925 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.11.0-1 [66.7 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-1 [388 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 67 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.27 [92.2 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 73 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 debhelper all 13.27 [940 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 gcc-14-base arm64 14.3.0-8 [52.1 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-4 [371 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libgfortran-15-dev arm64 15.2.0-4 [411 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-4 [76.9 MB] Get: 88 http://deb.debian.org/debian forky/main arm64 gfortran-15 arm64 15.2.0-4 [17.9 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4 [1280 B] Get: 90 http://deb.debian.org/debian forky/main arm64 gfortran arm64 4:15.2.0-4 [1428 B] Get: 91 http://deb.debian.org/debian forky/main arm64 libnl-3-200 arm64 3.11.0-2 [57.9 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libnl-route-3-200 arm64 3.11.0-2 [176 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libibverbs1 arm64 56.1-1+b1 [59.8 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 ibverbs-providers arm64 56.1-1+b1 [338 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 icu-devtools arm64 76.1-4 [200 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libllvm17t64 arm64 1:17.0.6-22+b3 [21.3 MB] Get: 99 http://deb.debian.org/debian forky/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 100 http://deb.debian.org/debian forky/main arm64 libdrm-common all 2.4.125-2 [8576 B] Get: 101 http://deb.debian.org/debian forky/main arm64 libdrm2 arm64 2.4.125-2 [38.4 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libdrm-amdgpu1 arm64 2.4.125-2 [22.3 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libhsakmt1 arm64 6.2.4+ds-1 [58.3 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libhsa-runtime64-1 arm64 6.1.2-3 [302 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libamdhip64-5 arm64 5.7.1-6 [8824 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libblas-dev arm64 3.12.1-7 [145 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgcc-14-dev arm64 14.3.0-8 [2364 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libstdc++-14-dev arm64 14.3.0-8 [2567 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libboost1.83-dev arm64 1.83.0-5 [10.6 MB] Get: 112 http://deb.debian.org/debian forky/main arm64 libboost-atomic1.83.0 arm64 1.83.0-5 [234 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libboost-atomic1.83-dev arm64 1.83.0-5 [235 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libboost-atomic-dev arm64 1.83.0.2+b2 [3892 B] Get: 115 http://deb.debian.org/debian forky/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-5 [240 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 libboost-chrono1.83-dev arm64 1.83.0-5 [245 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libboost-chrono-dev arm64 1.83.0.2+b2 [4212 B] Get: 118 http://deb.debian.org/debian forky/main arm64 libboost-container1.83.0 arm64 1.83.0-5 [259 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libboost-container1.83-dev arm64 1.83.0-5 [265 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libboost-container-dev arm64 1.83.0.2+b2 [4064 B] Get: 121 http://deb.debian.org/debian forky/main arm64 libboost-date-time1.83.0 arm64 1.83.0-5 [231 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libboost-serialization1.83.0 arm64 1.83.0-5 [325 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libboost-serialization1.83-dev arm64 1.83.0-5 [374 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libboost-date-time1.83-dev arm64 1.83.0-5 [239 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 libboost-system1.83.0 arm64 1.83.0-5 [231 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 libboost-system1.83-dev arm64 1.83.0-5 [232 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libboost-thread1.83.0 arm64 1.83.0-5 [266 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libboost-thread1.83-dev arm64 1.83.0-5 [277 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 libboost-context1.83.0 arm64 1.83.0-5 [232 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 libboost-context1.83-dev arm64 1.83.0-5 [233 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 libboost-context-dev arm64 1.83.0.2+b2 [3792 B] Get: 132 http://deb.debian.org/debian forky/main arm64 libboost-coroutine1.83.0 arm64 1.83.0-5 [235 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 libboost-coroutine1.83-dev arm64 1.83.0-5 [237 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 libboost-coroutine-dev arm64 1.83.0.2+b2 [3860 B] Get: 135 http://deb.debian.org/debian forky/main arm64 libboost-date-time-dev arm64 1.83.0.2+b2 [3584 B] Get: 136 http://deb.debian.org/debian forky/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 137 http://deb.debian.org/debian forky/main arm64 libboost-exception1.83-dev arm64 1.83.0-5 [230 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 libboost-exception-dev arm64 1.83.0.2+b2 [3572 B] Get: 139 http://deb.debian.org/debian forky/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-5 [273 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-5 [293 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 libboost-fiber1.83.0 arm64 1.83.0-5 [253 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 libboost-fiber1.83-dev arm64 1.83.0-5 [265 kB] Get: 143 http://deb.debian.org/debian forky/main arm64 libboost-fiber-dev arm64 1.83.0.2+b2 [4016 B] Get: 144 http://deb.debian.org/debian forky/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B] Get: 145 http://deb.debian.org/debian forky/main arm64 libboost-graph1.83.0 arm64 1.83.0-5 [342 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83.0 arm64 1.83.0-5 [314 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 libicu-dev arm64 76.1-4 [10.6 MB] Get: 148 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83-dev arm64 1.83.0-5 [335 kB] Get: 149 http://deb.debian.org/debian forky/main arm64 libboost-test1.83.0 arm64 1.83.0-5 [438 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 libboost-test1.83-dev arm64 1.83.0-5 [527 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 libboost-graph1.83-dev arm64 1.83.0-5 [373 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B] Get: 153 http://deb.debian.org/debian forky/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 librdmacm1t64 arm64 56.1-1+b1 [67.9 kB] Get: 156 http://deb.debian.org/debian forky/main arm64 libfabric1 arm64 2.1.0-1.1 [548 kB] Get: 157 http://deb.debian.org/debian forky/main arm64 libhwloc15 arm64 2.12.2-1 [142 kB] Get: 158 http://deb.debian.org/debian forky/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 159 http://deb.debian.org/debian forky/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 160 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 161 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 162 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 163 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 164 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 165 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 166 http://deb.debian.org/debian forky/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.7 kB] Get: 168 http://deb.debian.org/debian forky/main arm64 libhwloc-plugins arm64 2.12.2-1 [18.1 kB] Get: 169 http://deb.debian.org/debian forky/main arm64 libpmix2t64 arm64 6.0.0+really5.0.8-1 [574 kB] Get: 170 http://deb.debian.org/debian forky/main arm64 libibumad3 arm64 56.1-1+b1 [29.3 kB] Get: 171 http://deb.debian.org/debian forky/main arm64 libibmad5 arm64 56.1-1+b1 [42.8 kB] Get: 172 http://deb.debian.org/debian forky/main arm64 libucx0 arm64 1.19.0+ds-1 [1081 kB] Get: 173 http://deb.debian.org/debian forky/main arm64 libopenmpi40 arm64 5.0.8-10+b1 [2104 kB] Get: 174 http://deb.debian.org/debian forky/main arm64 libboost-mpi1.83.0 arm64 1.83.0-5 [268 kB] Get: 175 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel1.83.0 arm64 1.83.0-5 [276 kB] Get: 176 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel1.83-dev arm64 1.83.0-5 [284 kB] Get: 177 http://deb.debian.org/debian forky/main arm64 libboost-graph-parallel-dev arm64 1.83.0.2+b2 [3716 B] Get: 178 http://deb.debian.org/debian forky/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-5 [261 kB] Get: 179 http://deb.debian.org/debian forky/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 180 http://deb.debian.org/debian forky/main arm64 libboost-json1.83.0 arm64 1.83.0-5 [348 kB] Get: 181 http://deb.debian.org/debian forky/main arm64 libboost-json1.83-dev arm64 1.83.0-5 [372 kB] Get: 182 http://deb.debian.org/debian forky/main arm64 libboost-json-dev arm64 1.83.0.2+b2 [3696 B] Get: 183 http://deb.debian.org/debian forky/main arm64 libboost-locale1.83.0 arm64 1.83.0-5 [441 kB] Get: 184 http://deb.debian.org/debian forky/main arm64 libboost-locale1.83-dev arm64 1.83.0-5 [543 kB] Get: 185 http://deb.debian.org/debian forky/main arm64 libboost-locale-dev arm64 1.83.0.2+b2 [3916 B] Get: 186 http://deb.debian.org/debian forky/main arm64 libboost-log1.83.0 arm64 1.83.0-5 [644 kB] Get: 187 http://deb.debian.org/debian forky/main arm64 libboost-log1.83-dev arm64 1.83.0-5 [850 kB] Get: 188 http://deb.debian.org/debian forky/main arm64 libboost-log-dev arm64 1.83.0.2+b2 [3788 B] Get: 189 http://deb.debian.org/debian forky/main arm64 libboost-math1.83.0 arm64 1.83.0-5 [471 kB] Get: 190 http://deb.debian.org/debian forky/main arm64 libboost-math1.83-dev arm64 1.83.0-5 [536 kB] Get: 191 http://deb.debian.org/debian forky/main arm64 libboost-math-dev arm64 1.83.0.2+b2 [3784 B] Get: 192 http://deb.debian.org/debian forky/main arm64 openmpi-common all 5.0.8-10 [97.5 kB] Get: 193 http://deb.debian.org/debian forky/main arm64 libnl-3-dev arm64 3.11.0-2 [104 kB] Get: 194 http://deb.debian.org/debian forky/main arm64 libnl-route-3-dev arm64 3.11.0-2 [210 kB] Get: 195 http://deb.debian.org/debian forky/main arm64 libibverbs-dev arm64 56.1-1+b1 [649 kB] Get: 196 http://deb.debian.org/debian forky/main arm64 libnuma-dev arm64 2.0.19-1 [37.6 kB] Get: 197 http://deb.debian.org/debian forky/main arm64 libltdl7 arm64 2.5.4-5 [415 kB] Get: 198 http://deb.debian.org/debian forky/main arm64 libltdl-dev arm64 2.5.4-5 [168 kB] Get: 199 http://deb.debian.org/debian forky/main arm64 libhwloc-dev arm64 2.12.2-1 [239 kB] Get: 200 http://deb.debian.org/debian forky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 201 http://deb.debian.org/debian forky/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 202 http://deb.debian.org/debian forky/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 203 http://deb.debian.org/debian forky/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 204 http://deb.debian.org/debian forky/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 205 http://deb.debian.org/debian forky/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 206 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 207 http://deb.debian.org/debian forky/main arm64 openmpi-bin arm64 5.0.8-10+b1 [184 kB] Get: 208 http://deb.debian.org/debian forky/main arm64 libopenmpi-dev arm64 5.0.8-10+b1 [1090 kB] Get: 209 http://deb.debian.org/debian forky/main arm64 mpi-default-dev arm64 1.19 [3432 B] Get: 210 http://deb.debian.org/debian forky/main arm64 libboost-mpi1.83-dev arm64 1.83.0-5 [291 kB] Get: 211 http://deb.debian.org/debian forky/main arm64 libboost-mpi-dev arm64 1.83.0.2+b2 [3668 B] Get: 212 http://deb.debian.org/debian forky/main arm64 libboost-python1.83.0 arm64 1.83.0-5 [296 kB] Get: 213 http://deb.debian.org/debian forky/main arm64 mpi-default-bin arm64 1.19 [2640 B] Get: 214 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python1.83.0 arm64 1.83.0-5 [343 kB] Get: 215 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python1.83-dev arm64 1.83.0-5 [237 kB] Get: 216 http://deb.debian.org/debian forky/main arm64 libboost-mpi-python-dev arm64 1.83.0.2+b2 [3700 B] Get: 217 http://deb.debian.org/debian forky/main arm64 libboost-nowide1.83.0 arm64 1.83.0-5 [234 kB] Get: 218 http://deb.debian.org/debian forky/main arm64 libboost-nowide1.83-dev arm64 1.83.0-5 [236 kB] Get: 219 http://deb.debian.org/debian forky/main arm64 libboost-nowide-dev arm64 1.83.0.2+b2 [3660 B] Get: 220 http://deb.debian.org/debian forky/main arm64 libboost-numpy1.83.0 arm64 1.83.0-5 [241 kB] Get: 221 http://deb.debian.org/debian forky/main arm64 libboost-numpy1.83-dev arm64 1.83.0-5 [246 kB] Get: 222 http://deb.debian.org/debian forky/main arm64 libboost-numpy-dev arm64 1.83.0.2+b2 [3632 B] Get: 223 http://deb.debian.org/debian forky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-5 [331 kB] Get: 224 http://deb.debian.org/debian forky/main arm64 libboost-program-options1.83-dev arm64 1.83.0-5 [369 kB] Get: 225 http://deb.debian.org/debian forky/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 226 http://deb.debian.org/debian forky/main arm64 libpython3.13 arm64 3.13.7-1 [1978 kB] Get: 227 http://deb.debian.org/debian forky/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 228 http://deb.debian.org/debian forky/main arm64 libpython3.13-dev arm64 3.13.7-1 [4924 kB] Get: 229 http://deb.debian.org/debian forky/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 230 http://deb.debian.org/debian forky/main arm64 python3.13-dev arm64 3.13.7-1 [504 kB] Get: 231 http://deb.debian.org/debian forky/main arm64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 232 http://deb.debian.org/debian forky/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 233 http://deb.debian.org/debian forky/main arm64 libboost-python1.83-dev arm64 1.83.0-5 [322 kB] Get: 234 http://deb.debian.org/debian forky/main arm64 libboost-python-dev arm64 1.83.0.2+b2 [3880 B] Get: 235 http://deb.debian.org/debian forky/main arm64 libboost-random1.83.0 arm64 1.83.0-5 [238 kB] Get: 236 http://deb.debian.org/debian forky/main arm64 libboost-random1.83-dev arm64 1.83.0-5 [241 kB] Get: 237 http://deb.debian.org/debian forky/main arm64 libboost-random-dev arm64 1.83.0.2+b2 [3584 B] Get: 238 http://deb.debian.org/debian forky/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 239 http://deb.debian.org/debian forky/main arm64 libboost-serialization-dev arm64 1.83.0.2+b2 [3816 B] Get: 240 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace1.83.0 arm64 1.83.0-5 [277 kB] Get: 241 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace1.83-dev arm64 1.83.0-5 [245 kB] Get: 242 http://deb.debian.org/debian forky/main arm64 libboost-stacktrace-dev arm64 1.83.0.2+b2 [3580 B] Get: 243 http://deb.debian.org/debian forky/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 244 http://deb.debian.org/debian forky/main arm64 libboost-test-dev arm64 1.83.0.2+b2 [3620 B] Get: 245 http://deb.debian.org/debian forky/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 246 http://deb.debian.org/debian forky/main arm64 libboost-timer1.83.0 arm64 1.83.0-5 [235 kB] Get: 247 http://deb.debian.org/debian forky/main arm64 libboost-timer1.83-dev arm64 1.83.0-5 [237 kB] Get: 248 http://deb.debian.org/debian forky/main arm64 libboost-timer-dev arm64 1.83.0.2+b2 [3712 B] Get: 249 http://deb.debian.org/debian forky/main arm64 libboost1.83-tools-dev arm64 1.83.0-5 [1408 kB] Get: 250 http://deb.debian.org/debian forky/main arm64 libboost-tools-dev arm64 1.83.0.2+b2 [3764 B] Get: 251 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure1.83.0 arm64 1.83.0-5 [245 kB] Get: 252 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure1.83-dev arm64 1.83.0-5 [250 kB] Get: 253 http://deb.debian.org/debian forky/main arm64 libboost-type-erasure-dev arm64 1.83.0.2+b2 [3676 B] Get: 254 http://deb.debian.org/debian forky/main arm64 libboost-url1.83.0 arm64 1.83.0-5 [328 kB] Get: 255 http://deb.debian.org/debian forky/main arm64 libboost-url1.83-dev arm64 1.83.0-5 [423 kB] Get: 256 http://deb.debian.org/debian forky/main arm64 libboost-url-dev arm64 1.83.0.2+b2 [3720 B] Get: 257 http://deb.debian.org/debian forky/main arm64 libboost-wave1.83.0 arm64 1.83.0-5 [416 kB] Get: 258 http://deb.debian.org/debian forky/main arm64 libboost-wave1.83-dev arm64 1.83.0-5 [492 kB] Get: 259 http://deb.debian.org/debian forky/main arm64 libboost-wave-dev arm64 1.83.0.2+b2 [3616 B] Get: 260 http://deb.debian.org/debian forky/main arm64 libboost-all-dev arm64 1.83.0.2+b2 [3924 B] Get: 261 http://deb.debian.org/debian forky/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Get: 262 http://deb.debian.org/debian forky/main arm64 libcereal-dev arm64 1.3.2+dfsg-6 [221 kB] Get: 263 http://deb.debian.org/debian forky/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 264 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 265 http://deb.debian.org/debian forky/main arm64 liblapack-dev arm64 3.12.1-7 [3829 kB] Get: 266 http://deb.debian.org/debian forky/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 267 http://deb.debian.org/debian forky/main arm64 libmbedcrypto16 arm64 3.6.4-2 [346 kB] Get: 268 http://deb.debian.org/debian forky/main arm64 libmbedx509-7 arm64 3.6.4-2 [150 kB] Get: 269 http://deb.debian.org/debian forky/main arm64 libmbedtls21 arm64 3.6.4-2 [229 kB] Get: 270 http://deb.debian.org/debian forky/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 271 http://deb.debian.org/debian forky/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 272 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 273 http://deb.debian.org/debian forky/main arm64 libpng-dev arm64 1.6.50-1 [361 kB] Get: 274 http://deb.debian.org/debian forky/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 275 http://deb.debian.org/debian forky/main arm64 libspoa7.0.0 arm64 4.1.4-2+b1 [53.3 kB] Get: 276 http://deb.debian.org/debian forky/main arm64 libspoa-dev arm64 4.1.4-2+b1 [9788 B] Get: 277 http://deb.debian.org/debian forky/main arm64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 278 http://deb.debian.org/debian forky/main arm64 ncbi-blast+ arm64 2.16.0+ds-7 [14.5 MB] Get: 279 http://deb.debian.org/debian forky/main arm64 patchelf arm64 0.18.0-1.4 [89.3 kB] Get: 280 http://deb.debian.org/debian forky/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 281 http://deb.debian.org/debian forky/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 282 http://deb.debian.org/debian forky/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 283 http://deb.debian.org/debian forky/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 284 http://deb.debian.org/debian forky/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 285 http://deb.debian.org/debian forky/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 286 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.3-1 [123 kB] Get: 287 http://deb.debian.org/debian forky/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 288 http://deb.debian.org/debian forky/main arm64 python3-roman all 5.1-1 [11.0 kB] Get: 289 http://deb.debian.org/debian forky/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 290 http://deb.debian.org/debian forky/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 291 http://deb.debian.org/debian forky/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 292 http://deb.debian.org/debian forky/main arm64 python3-markupsafe arm64 3.0.2-2 [13.5 kB] Get: 293 http://deb.debian.org/debian forky/main arm64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 294 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 295 http://deb.debian.org/debian forky/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 296 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 297 http://deb.debian.org/debian forky/main arm64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 298 http://deb.debian.org/debian forky/main arm64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 299 http://deb.debian.org/debian forky/main arm64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 300 http://deb.debian.org/debian forky/main arm64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 301 http://deb.debian.org/debian forky/main arm64 sphinx-common all 8.2.3-6 [619 kB] Get: 302 http://deb.debian.org/debian forky/main arm64 python3-sphinx all 8.2.3-6 [477 kB] Fetched 282 MB in 2s (151 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20000 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.7-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_arm64.deb ... Unpacking python3.13 (3.13.7-1) ... 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Setting up libboost-program-options1.83.0:arm64 (1.83.0-5) ... Setting up libpciaccess0:arm64 (0.17-3+b3) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libboost-stacktrace1.83.0:arm64 (1.83.0-5) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up bsdextrautils (2.41.2-1) ... Setting up libboost-nowide1.83.0 (1.83.0-5) ... Setting up libboost-date-time1.83.0:arm64 (1.83.0-5) ... Setting up libboost-json1.83.0:arm64 (1.83.0-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libboost-timer1.83.0:arm64 (1.83.0-5) ... Setting up gcc-14-base:arm64 (14.3.0-8) ... Setting up libcbor0.10:arm64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libboost-regex1.83.0:arm64 (1.83.0-5) ... Setting up libdebhelper-perl (13.27) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up libboost-system1.83.0:arm64 (1.83.0-5) ... Setting up libuv1t64:arm64 (1.51.0-2) ... Setting up libboost-context1.83.0:arm64 (1.83.0-5) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libboost-random1.83.0:arm64 (1.83.0-5) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libibumad3:arm64 (56.1-1+b1) ... Setting up libboost-thread1.83.0:arm64 (1.83.0-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libibmad5:arm64 (56.1-1+b1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libboost-filesystem1.83.0:arm64 (1.83.0-5) ... Setting up libboost-url1.83.0:arm64 (1.83.0-5) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up rapidjson-dev (1.1.0+dfsg2-7.4) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libseqan2-dev (2.4.0+dfsg-16) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 2 10:34:29 UTC 2026. Universal Time is now: Mon Nov 2 10:34:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-5) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-5) ... Setting up libboost-numpy1.83.0 (1.83.0-5) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libmunge2:arm64 (0.5.16-1) ... Setting up libexpat1-dev:arm64 (2.7.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libboost-chrono1.83.0t64:arm64 (1.83.0-5) ... Setting up libjsoncpp26:arm64 (1.9.6-4) ... Setting up libproc2-0:arm64 (2:4.0.4-9) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libspoa7.0.0:arm64 (4.1.4-2+b1) ... Setting up libboost-nowide1.83-dev (1.83.0-5) ... Setting up libpng16-16t64:arm64 (1.6.50-1) ... Setting up libhwloc15:arm64 (2.12.2-1) ... Setting up autopoint (0.23.1-2) ... Setting up libboost-numpy1.83-dev (1.83.0-5) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libltdl7:arm64 (2.5.4-5) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up libboost-test1.83.0:arm64 (1.83.0-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (15.2.0-4) ... Setting up libboost-fiber1.83.0:arm64 (1.83.0-5) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.11.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up libnuma1:arm64 (2.0.19-1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.11.0-2) ... Setting up libboost-graph1.83.0:arm64 (1.83.0-5) ... Setting up openmpi-common (5.0.8-10) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libboost-container1.83.0:arm64 (1.83.0-5) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libboost-type-erasure1.83.0:arm64 (1.83.0-5) ... Setting up cmake-data (4.1.1+really3.31.6-2) ... Setting up librhash1:arm64 (1.4.6-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libicu76:arm64 (76.1-4) ... Setting up libmbedcrypto16:arm64 (3.6.4-2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libboost-math1.83.0:arm64 (1.83.0-5) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libgcc-14-dev:arm64 (14.3.0-8) ... Setting up patchelf (0.18.0-1.4) ... Setting up libfido2-1:arm64 (1.16.0-2) ... Setting up openssl (3.5.3-1) ... Setting up libstdc++-14-dev:arm64 (14.3.0-8) ... Setting up libdrm-common (2.4.125-2) ... Setting up libarchive13t64:arm64 (3.7.4-4+b1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libboost1.83-tools-dev (1.83.0-5) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libboost-wave1.83.0:arm64 (1.83.0-5) ... Setting up libboost1.83-dev:arm64 (1.83.0-5) ... Setting up gettext (0.23.1-2+b1) ... Setting up libboost-coroutine1.83.0:arm64 (1.83.0-5) ... Setting up libboost-chrono1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-math1.83-dev:arm64 (1.83.0-5) ... Setting up libtool (2.5.4-5) ... Setting up libboost-chrono-dev:arm64 (1.83.0.2+b2) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libboost-log1.83.0 (1.83.0-5) ... Setting up libboost-math-dev:arm64 (1.83.0.2+b2) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libpng-dev:arm64 (1.6.50-1) ... Setting up libboost-program-options1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-serialization1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-locale1.83.0:arm64 (1.83.0-5) ... Setting up libcereal-dev:arm64 (1.3.2+dfsg-6) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libboost-test1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-tools-dev (1.83.0.2+b2) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up libboost-nowide-dev (1.83.0.2+b2) ... Setting up libgfortran-15-dev:arm64 (15.2.0-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.19-1) ... Setting up libnl-route-3-200:arm64 (3.11.0-2) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ... Setting up libboost-test-dev:arm64 (1.83.0.2+b2) ... Setting up dh-autoreconf (21) ... Setting up libltdl-dev:arm64 (2.5.4-5) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libmbedx509-7:arm64 (3.6.4-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:arm64 (1.83.0-5) ... Setting up libllvm17t64:arm64 (1:17.0.6-22+b3) ... Setting up libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Setting up gfortran-15-aarch64-linux-gnu (15.2.0-4) ... Setting up libboost-container1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-date-time1.83-dev:arm64 (1.83.0-5) ... Setting up sphinx-common (8.2.3-6) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libboost-numpy-dev (1.83.0.2+b2) ... Setting up liblapack-dev:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libboost-stacktrace1.83-dev:arm64 (1.83.0-5) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up libboost-serialization-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-date-time-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-atomic1.83-dev:arm64 (1.83.0-5) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libmbedtls21:arm64 (3.6.4-2) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libboost-atomic-dev:arm64 (1.83.0.2+b2) ... Setting up libdrm2:arm64 (2.4.125-2) ... Setting up libnl-3-dev:arm64 (3.11.0-2) ... Setting up libboost-exception1.83-dev:arm64 (1.83.0-5) ... Setting up groff-base (1.23.0-9) ... Setting up libboost-stacktrace-dev:arm64 (1.83.0.2+b2) ... Setting up xml-core (0.19) ... Setting up gfortran-aarch64-linux-gnu (4:15.2.0-4) ... Setting up libhwloc-dev:arm64 (2.12.2-1) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libboost-system1.83-dev:arm64 (1.83.0-5) ... Setting up libpython3.13-stdlib:arm64 (3.13.7-1) ... Setting up libicu-dev:arm64 (76.1-4) ... Setting up libboost-timer-dev:arm64 (1.83.0.2+b2) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.125-2) ... Setting up libpython3.13:arm64 (3.13.7-1) ... Setting up libgnutls30t64:arm64 (3.8.9-3) ... Setting up libboost-thread1.83-dev:arm64 (1.83.0-5) ... Setting up libibverbs1:arm64 (56.1-1+b1) ... Setting up libboost-json1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-locale1.83-dev:arm64 (1.83.0-5) ... Setting up ibverbs-providers:arm64 (56.1-1+b1) ... Setting up libspoa-dev:arm64 (4.1.4-2+b1) ... Setting up python3.13 (3.13.7-1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-system-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-type-erasure1.83-dev:arm64 (1.83.0-5) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up libboost-url1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-locale-dev:arm64 (1.83.0.2+b2) ... Setting up python3 (3.13.7-1) ... Setting up libboost-filesystem1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-exception-dev:arm64 (1.83.0.2+b2) ... Setting up libhwloc-plugins:arm64 (2.12.2-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (3.0.2-2) ... Setting up gfortran (4:15.2.0-4) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libboost-container-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-type-erasure-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-context1.83-dev:arm64 (1.83.0-5) ... Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up libnl-route-3-dev:arm64 (3.11.0-2) ... Setting up libboost-coroutine1.83-dev:arm64 (1.83.0-5) ... Setting up python3-roman (5.1-1) ... Setting up python3-jinja2 (3.1.6-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up libboost-fiber1.83-dev:arm64 (1.83.0-5) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up python3-snowballstemmer (3.0.1-1) ... Setting up libpython3.13-dev:arm64 (3.13.7-1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up python3-idna (3.10-1) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-5) ... Setting up libboost-random1.83-dev:arm64 (1.83.0-5) ... Setting up libpmix2t64:arm64 (6.0.0+really5.0.8-1) ... Setting up python3-urllib3 (2.5.0-1) ... Setting up librdmacm1t64:arm64 (56.1-1+b1) ... Setting up python3-roman-numerals (3.1.0-2) ... Setting up libboost-url-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-coroutine-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-log1.83-dev (1.83.0-5) ... Setting up libboost-json-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-regex-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-log-dev (1.83.0.2+b2) ... Setting up libboost-filesystem-dev:arm64 (1.83.0.2+b2) ... Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... Setting up libboost-thread-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-fiber-dev:arm64 (1.83.0.2+b2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up dh-python (6.20250414) ... Setting up libfabric1:arm64 (2.1.0-1.1) ... Setting up libpython3-dev:arm64 (3.13.7-1) ... Setting up libboost-wave1.83-dev:arm64 (1.83.0-5) ... Setting up libcurl4t64:arm64 (8.16.0-1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up libboost-iostreams1.83-dev:arm64 (1.83.0-5) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up libboost-random-dev:arm64 (1.83.0.2+b2) ... Setting up debhelper (13.27) ... Setting up dh-exec (0.30+b1) ... Setting up libboost-wave-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-context-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-iostreams-dev:arm64 (1.83.0.2+b2) ... Setting up libibverbs-dev:arm64 (56.1-1+b1) ... Setting up libboost-graph1.83-dev:arm64 (1.83.0-5) ... Setting up pybind11-dev (2.13.6-2) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-requests (2.32.5+dfsg-1) ... Setting up libboost-python1.83-dev (1.83.0-5) ... Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... Setting up cmake (4.1.1+really3.31.6-2) ... Setting up python3-pybind11 (2.13.6-2) ... Setting up libboost-graph-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up libamdhip64-5:arm64 (5.7.1-6) ... Setting up libucx0:arm64 (1.19.0+ds-1) ... Setting up libopenmpi40:arm64 (5.0.8-10+b1) ... Setting up libboost-mpi1.83.0 (1.83.0-5) ... Setting up openmpi-bin (5.0.8-10+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libboost-graph-parallel1.83.0 (1.83.0-5) ... Setting up mpi-default-bin (1.19) ... Setting up libopenmpi-dev:arm64 (5.0.8-10+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-5) ... Setting up libboost-mpi-python1.83.0 (1.83.0-5) ... Setting up libboost-graph-parallel-dev (1.83.0.2+b2) ... Setting up mpi-default-dev (1.19) ... Setting up libboost-mpi1.83-dev (1.83.0-5) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-5) ... Setting up libboost-mpi-python-dev (1.83.0.2+b2) ... Setting up libboost-all-dev (1.83.0.2+b2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.2.3-6) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shasta-0.12.0/ && 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_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is aarch64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (1.1s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' 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/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/Align4.cpp [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Align4.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Assembler.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Assembler.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/Align4.cpp:15: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/Align4.cpp:15: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp:9: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp:4: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp [ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp:7: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp:4: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp:6: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp:7: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 16%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 16%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 16%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 17%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/seqan.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp:6: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp:25: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ In file included from /usr/include/c++/15/bits/exception_ptr.h:41, from /usr/include/c++/15/exception:168, from /usr/include/c++/15/ios:43, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1274:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46: 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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1264:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1295:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1285:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ [ 17%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1094:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1084:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1114:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1104:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp:25: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp In file included from /usr/include/c++/15/bits/exception_ptr.h:41, from /usr/include/c++/15/exception:168, from /usr/include/c++/15/ios:43, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1274:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46: 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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1264:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1295:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1285:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1094:29: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1084:48: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 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++/15/bits/stl_algobase.h:186:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1046:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/15/bits/stl_algo.h:1073:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1114:33: /usr/include/c++/15/bits/move.h:237:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 237 | __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++/15/bits/allocator.h:203:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, 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++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/stl_vector.h:587:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1104:53: /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset 9223372036854775802 into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/15/bits/new_allocator.h:151:73: note: at offset [9223372036854775801, 9223372036854775802] into destination object of size [1, 9223372036854775807] allocated by ‘operator new’ [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 623 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 623 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 26%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY 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-DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp:10: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY 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/usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 28%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp [ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp:10: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp:29: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 34%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp [ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.cpp [ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp [ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/ConfigurationTable.cpp [ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/ConsensusCaller.cpp [ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMode3.cpp [ 37%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Coverage.cpp [ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Histogram.cpp [ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/HashedKmerChecker.cpp [ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/HttpServer.cpp [ 39%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/InducedAlignment.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerCheckerFactory.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp [ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp [ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::id’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::minMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 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-I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp:29: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 58%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PythonModule.cpp [ 59%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp [ 59%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReadGraph.cpp [ 60%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReadLoader.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:114:44: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::createEdges(const shasta::mode0::AssemblyGraph&, const std::vector&)’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::id’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::minMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.cpp [ 60%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/Reads.cpp [ 60%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/ReferenceOverlapMap.cpp [ 61%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp [ 62%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.cpp [ 62%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0.cpp [ 62%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasedComponent.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp:17: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp [ 85%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/longestPath.cpp [ 92%] Building CXX object 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/build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp In file included from /usr/include/seqan/platform.h:44, from /usr/include/seqan/basic.h:42, from /usr/include/seqan/align.h:55, from /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp:17: /usr/include/c++/15/ciso646:49:6: warning: #warning " is not a standard header since C++20, use to detect implementation-specific macros" [-Wcpp] 49 | # warning " is not a standard header since C++20, use to detect implementation-specific macros" | ^~~~~~~ [ 96%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PrimaryGraph.cpp [ 96%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/performanceLog.cpp [ 96%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/platformDependent.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/runCommandWithTimeout.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/shastaLapack.cpp [ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/src/timestamp.cpp [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp [ 99%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/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/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/shastaDynamicLibrary.dir/link.d -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 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/s/usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libpng.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libboost_program_options.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libboost_serialization.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libspoa.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libpython3.13.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. 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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/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.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 -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.13 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [ 99%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -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/reproducible-path/shasta-0.12.0/srcMain/main.cpp [100%] Linking CXX static library shasta.a cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /build/reproducible-path/shasta-0.12.0/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 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/AssemblerAlign5.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" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o 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/HashedKmerChecker.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/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.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/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.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/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/Mode3Assembler.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/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.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/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Built target shastaStaticLibrary [100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/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/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/shastaDynamicExecutable.dir/link.d CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lpthread -lpython3.13 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' # 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 PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v8.2.3 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/sidebar.js Writing evaluated template result to /build/reproducible-path/shasta-0.12.0/build/html/_static/classic.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/shasta.a -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/shasta.so -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/shastaDynamic -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AlignOrientedReads.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AlignOrientedReads1.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AlignOrientedReads4.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AnalyzeAlignmentMatrix.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AnalyzeAssemblyGraphBubbles.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AnalyzeReadGraph.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/Assemble.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AssembleMarkerGraphEdges.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AssembleMarkerGraphVertices.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/AssembleSegment.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CheckConfigurations.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CheckMarkerGraphIsStrandSymmetric.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CleanupDuplicateMarkers.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/CleanupRunDirectory.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/ClusterMarkerGraphEdgeOrientedReads.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/ColorGfaBySimilarityToSegment.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/ColorGfaKeySegments.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/bin/ColorGfaWithTwoReads.py -- Installing: 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Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/./shasta-install/docs/Acknowledgments.html make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:421: renaming shasta.so to shasta.cpython-313-aarch64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' patchelf \ --set-soname shasta.cpython-313-aarch64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/reproducible-path/shasta-0.12.0 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a dwz: dwz: debian/shasta/usr/bin/shasta: .debug_info section not present debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-313-aarch64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_arm64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_arm64.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_arm64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/1060093 and its subdirectories I: Current time: Sun Nov 1 22:40:41 -12 2026 I: pbuilder-time-stamp: 1793616041 Tue Sep 30 04:17:43 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_1-100690.service; invocation ID: e20cf61314b347ff9dc48f1e029de238 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/shasta_0.12.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/shasta_0.12.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/shasta_0.12.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/b1/shasta_0.12.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9zSIZHr1/b2/shasta_0.12.0-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 202ms CPU time consumed: 170ms Memory peak: 17.5M (swap: 0B) Tue Sep 30 04:17:44 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 30 04:17:44 UTC 2025 I: shasta from forky built successfully and reproducibly on arm64. Tue Sep 30 04:17:45 UTC 2025 I: Removing signed shasta_0.12.0-1_arm64.buildinfo.asc files: removed './b1/shasta_0.12.0-1_arm64.buildinfo.asc' removed './b2/shasta_0.12.0-1_arm64.buildinfo.asc'