Wed Jun 19 13:23:08 UTC 2024 I: starting to build shasta/unstable/arm64 on jenkins on '2024-06-19 13:22' Wed Jun 19 13:23:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_22/17901/console.log Wed Jun 19 13:23:08 UTC 2024 I: Downloading source for unstable/shasta=0.12.0-1 --2024-06-19 13:23:08-- 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% 314M=0s 2024-06-19 13:23:08 (314 MB/s) - ‘shasta_0.12.0-1.dsc’ saved [2556/2556] Wed Jun 19 13:23:08 UTC 2024 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----- Wed Jun 19 13:23:08 UTC 2024 I: Checking whether the package is not for us Wed Jun 19 13:23:08 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Jun 19 13:23:08 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Wed Jun 19 13:30:35 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 19 01:23:11 -12 2024 I: pbuilder-time-stamp: 1718803391 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 gpgv: Signature made Sun May 26 16:21:26 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key 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/1384070/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d7198ed4cef246c58df457d8d5f1b59a' 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='1384070' 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.zopMsMVp/pbuilderrc_K5fw --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1384070/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 ... 19809 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} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-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} libbsd0{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} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{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} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmunge2{a} libnghttp2-14{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} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{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} 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-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-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 lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 295 newly installed, 0 to remove and 0 not upgraded. Need to get 201 MB of archives. After unpacking 1133 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.23 [24.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.2-1 [1327 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-15 [159 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.1-8.1 [95.1 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-2 [1394 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240517-1 [88.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-1.2 [27.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1 [74.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.2-1 [31.8 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.2-1 [80.4 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.2-1 [307 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.2-1 [125 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.7p1-5 [902 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-15 [683 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg-3 [609 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.2-2.1 [320 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-1 [173 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.62.1-1 [71.2 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-5 [207 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.8.0-1 [411 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-4 [142 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.29.5-1 [2168 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.29.5-1 [9060 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.16 [88.6 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 69 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-15 [1249 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.16 [891 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30 [25.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240422 [107 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.1.0-1 [361 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libgfortran-13-dev arm64 13.2.0-25 [401 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-25 [8827 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 gfortran-13 arm64 13.2.0-25 [12.8 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7 [1288 B] Get: 88 http://deb.debian.org/debian unstable/main arm64 gfortran arm64 4:13.2.0-7 [1428 B] Get: 89 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 52.0-1 [58.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 52.0-1 [316 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-4+b1 [194 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.121-2 [7972 B] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.121-2 [37.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.121-2 [21.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 5.7.1-2 [276 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-3 [8698 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.0-3 [98.2 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3 [10.6 MB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83.0 arm64 1.83.0-3 [233 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83-dev arm64 1.83.0-3 [234 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libboost-atomic-dev arm64 1.83.0.2+b2 [3892 B] Get: 110 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-3 [239 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83-dev arm64 1.83.0-3 [244 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libboost-chrono-dev arm64 1.83.0.2+b2 [4212 B] Get: 113 http://deb.debian.org/debian unstable/main arm64 libboost-container1.83.0 arm64 1.83.0-3 [258 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libboost-container1.83-dev arm64 1.83.0-3 [264 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libboost-container-dev arm64 1.83.0.2+b2 [4064 B] Get: 116 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83.0 arm64 1.83.0-3 [230 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83.0 arm64 1.83.0-3 [324 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83-dev arm64 1.83.0-3 [372 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83-dev arm64 1.83.0-3 [239 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-3 [230 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-3 [231 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83.0 arm64 1.83.0-3 [265 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83-dev arm64 1.83.0-3 [276 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libboost-context1.83.0 arm64 1.83.0-3 [231 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libboost-context1.83-dev arm64 1.83.0-3 [232 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libboost-context-dev arm64 1.83.0.2+b2 [3792 B] Get: 127 http://deb.debian.org/debian unstable/main arm64 libboost-coroutine1.83.0 arm64 1.83.0-3 [234 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libboost-coroutine1.83-dev arm64 1.83.0-3 [236 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libboost-coroutine-dev arm64 1.83.0.2+b2 [3860 B] Get: 130 http://deb.debian.org/debian unstable/main arm64 libboost-date-time-dev arm64 1.83.0.2+b2 [3584 B] Get: 131 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 132 http://deb.debian.org/debian unstable/main arm64 libboost-exception1.83-dev arm64 1.83.0-3 [230 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libboost-exception-dev arm64 1.83.0.2+b2 [3572 B] Get: 134 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-3 [273 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-3 [291 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libboost-fiber1.83.0 arm64 1.83.0-3 [252 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libboost-fiber1.83-dev arm64 1.83.0-3 [264 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libboost-fiber-dev arm64 1.83.0.2+b2 [4016 B] Get: 139 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B] Get: 140 http://deb.debian.org/debian unstable/main arm64 libboost-graph1.83.0 arm64 1.83.0-3 [342 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-3 [311 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-4+b1 [10.2 MB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-3 [333 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libboost-test1.83.0 arm64 1.83.0-3 [435 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libboost-test1.83-dev arm64 1.83.0-3 [526 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libboost-graph1.83-dev arm64 1.83.0-3 [375 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B] Get: 148 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10 [125 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [54.1 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 52.0-1 [66.5 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.2-3 [580 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 52.0-1 [26.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 52.0-1 [41.4 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.17.0+ds-1 [955 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libboost-mpi1.83.0 arm64 1.83.0-3 [267 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libboost-graph-parallel1.83.0 arm64 1.83.0-3 [275 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libboost-graph-parallel1.83-dev arm64 1.83.0-3 [283 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libboost-graph-parallel-dev arm64 1.83.0.2+b2 [3716 B] Get: 173 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-3 [260 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 175 http://deb.debian.org/debian unstable/main arm64 libboost-json1.83.0 arm64 1.83.0-3 [347 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libboost-json1.83-dev arm64 1.83.0-3 [368 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libboost-json-dev arm64 1.83.0.2+b2 [3696 B] Get: 178 http://deb.debian.org/debian unstable/main arm64 libboost-locale1.83.0 arm64 1.83.0-3 [436 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libboost-locale1.83-dev arm64 1.83.0-3 [539 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libboost-locale-dev arm64 1.83.0.2+b2 [3916 B] Get: 181 http://deb.debian.org/debian unstable/main arm64 libboost-log1.83.0 arm64 1.83.0-3 [641 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libboost-log1.83-dev arm64 1.83.0-3 [851 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libboost-log-dev arm64 1.83.0.2+b2 [3788 B] Get: 184 http://deb.debian.org/debian unstable/main arm64 libboost-math1.83.0 arm64 1.83.0-3 [463 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libboost-math1.83-dev arm64 1.83.0-3 [518 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libboost-math-dev arm64 1.83.0.2+b2 [3784 B] Get: 187 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3 [101 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [197 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 52.0-1 [630 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1 [37.4 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-7+b1 [165 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.10.0-1+b1 [234 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [169 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10 [102 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10 [60.0 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10 [303 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.2-3 [3921 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.15 [3152 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 libboost-mpi1.83-dev arm64 1.83.0-3 [290 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libboost-mpi-dev arm64 1.83.0.2+b2 [3668 B] Get: 208 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83.0 arm64 1.83.0-3 [333 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 mpi-default-bin arm64 1.15 [2408 B] Get: 210 http://deb.debian.org/debian unstable/main arm64 libboost-mpi-python1.83.0 arm64 1.83.0-3 [405 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libboost-mpi-python1.83-dev arm64 1.83.0-3 [239 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libboost-mpi-python-dev arm64 1.83.0.2+b2 [3700 B] Get: 213 http://deb.debian.org/debian unstable/main arm64 libboost-nowide1.83.0 arm64 1.83.0-3 [234 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libboost-nowide1.83-dev arm64 1.83.0-3 [236 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libboost-nowide-dev arm64 1.83.0.2+b2 [3660 B] Get: 216 http://deb.debian.org/debian unstable/main arm64 libboost-numpy1.83.0 arm64 1.83.0-3 [245 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libboost-numpy1.83-dev arm64 1.83.0-3 [252 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libboost-numpy-dev arm64 1.83.0.2+b2 [3632 B] Get: 219 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83.0 arm64 1.83.0-3 [332 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83-dev arm64 1.83.0-3 [369 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 222 http://deb.debian.org/debian unstable/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 226 http://deb.debian.org/debian unstable/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.2.6-9 [150 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83-dev arm64 1.83.0-3 [371 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libboost-python-dev arm64 1.83.0.2+b2 [3880 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 libboost-random1.83.0 arm64 1.83.0-3 [237 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libboost-random1.83-dev arm64 1.83.0-3 [240 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libboost-random-dev arm64 1.83.0.2+b2 [3584 B] Get: 235 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 236 http://deb.debian.org/debian unstable/main arm64 libboost-serialization-dev arm64 1.83.0.2+b2 [3816 B] Get: 237 http://deb.debian.org/debian unstable/main arm64 libboost-stacktrace1.83.0 arm64 1.83.0-3 [274 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libboost-stacktrace1.83-dev arm64 1.83.0-3 [244 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libboost-stacktrace-dev arm64 1.83.0.2+b2 [3580 B] Get: 240 http://deb.debian.org/debian unstable/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 241 http://deb.debian.org/debian unstable/main arm64 libboost-test-dev arm64 1.83.0.2+b2 [3620 B] Get: 242 http://deb.debian.org/debian unstable/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 243 http://deb.debian.org/debian unstable/main arm64 libboost-timer1.83.0 arm64 1.83.0-3 [234 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libboost-timer1.83-dev arm64 1.83.0-3 [236 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libboost-timer-dev arm64 1.83.0.2+b2 [3712 B] Get: 246 http://deb.debian.org/debian unstable/main arm64 libboost1.83-tools-dev arm64 1.83.0-3 [1386 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libboost-tools-dev arm64 1.83.0.2+b2 [3764 B] Get: 248 http://deb.debian.org/debian unstable/main arm64 libboost-type-erasure1.83.0 arm64 1.83.0-3 [244 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libboost-type-erasure1.83-dev arm64 1.83.0-3 [249 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libboost-type-erasure-dev arm64 1.83.0.2+b2 [3676 B] Get: 251 http://deb.debian.org/debian unstable/main arm64 libboost-url1.83.0 arm64 1.83.0-3 [325 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libboost-url1.83-dev arm64 1.83.0-3 [421 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libboost-url-dev arm64 1.83.0.2+b2 [3720 B] Get: 254 http://deb.debian.org/debian unstable/main arm64 libboost-wave1.83.0 arm64 1.83.0-3 [414 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libboost-wave1.83-dev arm64 1.83.0-3 [488 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libboost-wave-dev arm64 1.83.0.2+b2 [3616 B] Get: 257 http://deb.debian.org/debian unstable/main arm64 libboost-all-dev arm64 1.83.0.2+b2 [3924 B] Get: 258 http://deb.debian.org/debian unstable/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libcereal-dev arm64 1.3.2+dfsg-5 [221 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.0-3 [3584 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 liblmdb0 arm64 0.9.31-1+b1 [43.0 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libpng-dev arm64 1.6.43-5 [356 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libspoa7.0.0 arm64 4.1.4-1 [50.0 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libspoa-dev arm64 4.1.4-1 [9380 B] Get: 272 http://deb.debian.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 ncbi-blast+ arm64 2.12.0+ds-4+b1 [11.6 MB] Get: 274 http://deb.debian.org/debian unstable/main arm64 patchelf arm64 0.18.0-1.1 [86.6 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.12.0-1 [198 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.6.2-1 [157 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 python3-roman all 3.3-3 [9880 B] Get: 283 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.6-2.1 [38.6 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 286 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.12.0-1 [208 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.2.6-9 [702 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.2.6-9 [552 kB] Fetched 201 MB in 1s (157 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19809 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20125 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21117 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.23_all.deb ... Unpacking sensible-utils (0.0.23) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.2.2-1_arm64.deb ... Unpacking openssl (3.2.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-15_arm64.deb ... Unpacking gettext-base (0.21-15) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.1-8.1_arm64.deb ... Unpacking bsdextrautils (2.40.1-8.1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.12.1-2_arm64.deb ... Unpacking man-db (2.12.1-2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../016-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../017-libedit2_3.1-20240517-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240517-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../018-libcbor0.10_0.10.2-1.2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-1.2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../019-libfido2-1_1.15.0-1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../020-libkrb5support0_1.21.2-1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.2-1) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../021-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../022-libk5crypto3_1.21.2-1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.2-1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../023-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../024-libkrb5-3_1.21.2-1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.2-1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../025-libgssapi-krb5-2_1.21.2-1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.2-1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../026-openssh-client_1%3a9.7p1-5_arm64.deb ... Unpacking openssh-client (1:9.7p1-5) ... Selecting previously unselected package m4. Preparing to unpack .../027-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../028-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../029-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../030-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../031-autopoint_0.21-15_all.deb ... Unpacking autopoint (0.21-15) ... Selecting previously unselected package chrpath. Preparing to unpack .../032-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../033-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../034-libxml2_2.12.7+dfsg-3_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg-3) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../035-libarchive13t64_3.7.2-2.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.2-2.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../036-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../037-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../038-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../039-libldap-2.5-0_2.5.18+dfsg-1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../040-libnghttp2-14_1.62.1-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.62.1-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../041-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../042-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../043-libssh2-1t64_1.11.0-5_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-5) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../044-libcurl4t64_8.8.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.8.0-1) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../045-libjsoncpp25_1.9.5-6+b2_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../046-librhash0_1.4.3-3+b1_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../047-libuv1t64_1.48.0-4_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../048-cmake-data_3.29.5-1_all.deb ... 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Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 19 13:24:27 UTC 2024. Universal Time is now: Wed Jun 19 13:24:27 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-3) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-3) ... Setting up libboost-numpy1.83.0 (1.83.0-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libblas3:arm64 (3.12.0-3) ... 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 (0.5.15-4) ... Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libboost-chrono1.83.0t64:arm64 (1.83.0-3) ... 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Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libboost-system1.83-dev:arm64 (1.83.0-3) ... Setting up libssh2-1t64:arm64 (1.11.0-5) ... Setting up libboost-math1.83.0:arm64 (1.83.0-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up patchelf (0.18.0-1.1) ... Setting up libfido2-1:arm64 (1.15.0-1) ... Setting up libgfortran-13-dev:arm64 (13.2.0-25) ... Setting up openssl (3.2.2-1) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdrm-common (2.4.121-2) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:arm64 (72.1-4+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg-3) ... Setting up libboost1.83-tools-dev (1.83.0-3) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:arm64 (3.12.0-3) ... 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 libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... 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 (1.83.0-3) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up gettext (0.21-15) ... Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... Setting up libboost-coroutine1.83.0:arm64 (1.83.0-3) ... Setting up libboost-chrono1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-math1.83-dev:arm64 (1.83.0-3) ... Setting up libtool (2.4.7-7) ... Setting up libboost-chrono-dev:arm64 (1.83.0.2+b2) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libboost-log1.83.0 (1.83.0-3) ... Setting up libboost-math-dev:arm64 (1.83.0.2+b2) ... Setting up libedit2:arm64 (3.1-20240517-1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libboost-system-dev:arm64 (1.83.0.2+b2) ... Setting up libpng-dev:arm64 (1.6.43-5) ... Setting up libboost-serialization1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-locale1.83.0:arm64 (1.83.0-3) ... Setting up libcereal-dev (1.3.2+dfsg-5) ... Setting up libboost-test1.83-dev:arm64 (1.83.0-3) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-25) ... Setting up libboost-url1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-tools-dev (1.83.0.2+b2) ... Setting up libboost-filesystem1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-exception-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-nowide-dev (1.83.0.2+b2) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up libboost-test-dev:arm64 (1.83.0.2+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-7+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:arm64 (1.83.0-3) ... Setting up libllvm17t64:arm64 (1:17.0.6-12) ... Setting up libboost-container1.83-dev:arm64 (1.83.0-3) ... Setting up gfortran-13 (13.2.0-25) ... Setting up libboost-date-time1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-numpy-dev (1.83.0.2+b2) ... Setting up liblapack-dev:arm64 (3.12.0-3) ... 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 libgssapi-krb5-2:arm64 (1.21.2-1) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-3) ... Setting up libboost-random1.83-dev:arm64 (1.83.0-3) ... 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 libjs-sphinxdoc (7.2.6-9) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:arm64 (2.4.121-2) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up libmbedtls14t64:arm64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7) ... Setting up libboost-url-dev:arm64 (1.83.0.2+b2) ... Setting up libhwloc-dev:arm64 (2.10.0-1+b1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libboost-regex-dev:arm64 (1.83.0.2+b2) ... Setting up libarchive13t64:arm64 (3.7.2-2.1) ... 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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 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 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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 (1.4s) -- Generating done (0.0s) 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[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend 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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-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 make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [ 2%] 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 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-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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.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/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 [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o [ 5%] 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/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 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 [ 5%] 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/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/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 [ 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c 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/build/reproducible-path/shasta-0.12.0/src/Assembler.cpp [ 6%] 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 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 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/python3.11 -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 [ 7%] 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 [ 7%] 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 /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/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/python3.11 -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 /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); | ~~~^~~~ [ 9%] 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 [ 9%] 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 [ 10%] 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 [ 10%] 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/python3.11 -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 [ 10%] 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 [ 11%] 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 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-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 [ 12%] 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 [ 13%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 13%] 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 [ 14%] 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 [ 14%] 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 [ 14%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 15%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp [ 16%] 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 [ 16%] 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 [ 17%] 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 [ 17%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 17%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp In file included from /usr/include/c++/13/bits/exception_ptr.h:41, from /usr/include/c++/13/exception:164, from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, 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++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44: 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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ [ 17%] 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 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++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ [ 18%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 18%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 19%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 19%] 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 [ 20%] 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 [ 20%] 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/python3.11 -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 [ 20%] 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 [ 21%] 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 In file included from /usr/include/c++/13/bits/exception_ptr.h:41, from /usr/include/c++/13/exception:164, from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, 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++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In file included from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44: 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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, 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++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __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++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, 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++/13/bits/stl_vector.h:381:33, 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++/13/bits/stl_vector.h:398:44, 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++/13/bits/stl_vector.h:335:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:557:47, 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++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ [ 21%] 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 /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)); | ^~~~~~~~ [ 22%] 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/python3.11 -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 [ 23%] 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 [ 23%] 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 [ 24%] 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 [ 24%] 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/python3.11 -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 [ 24%] 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/python3.11 -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 [ 24%] 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 [ 25%] 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/python3.11 -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 [ 25%] 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 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-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 [ 29%] 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 /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)); | ^~~~~~~~ [ 30%] 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 [ 30%] 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 [ 31%] 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 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-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 32%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 33%] 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 [ 33%] 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 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/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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 34%] 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 [ 34%] 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 -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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 34%] 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 [ 35%] 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 [ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd 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/build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 36%] 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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF 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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 [ 37%] 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 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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 [ 40%] 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 [ 41%] 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 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-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 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/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/python3.11 -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 [ 43%] 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 [ 43%] 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/python3.11 -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 [ 44%] 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 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/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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 45%] Building CXX object 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/build/reproducible-path/shasta-0.12.0/src/LocalReadGraph.cpp [ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.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/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -c 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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/python3.11 -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 CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/runCommandWithTimeout.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/shastaLapack.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSpoa.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.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/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/timestamp.cpp [ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.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/python3.11 -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 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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/shastaDynamicLibrary.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 -lpython3.11 -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 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 -lpython3.11 -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 v7.2.6 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). making output directory... done WARNING: html_static_path entry '_static' does not exist 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... done copying extra files... done 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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/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:418: renaming shasta.so to shasta.cpython-311-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-311-aarch64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-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: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-aarch64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present 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-311-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 'shasta' in '../shasta_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 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_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/1384070 and its subdirectories I: Current time: Wed Jun 19 01:30:33 -12 2024 I: pbuilder-time-stamp: 1718803833 Wed Jun 19 13:30:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Wed Jun 19 13:30:36 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Wed Jun 19 13:35:04 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Wed Jun 19 13:35:05 UTC 2024 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: 28d381f9d336f7fc6d12551769a7fbd2e378154c 135820 python3-shasta-dbgsym_0.12.0-1_arm64.deb 6ce3075ecce5c22262302dac0a690d0eabe93f51 24032 python3-shasta-doc_0.12.0-1_all.deb bd8dafd991067bd260de292e26d0e0276f1a95f5 1913208 python3-shasta_0.12.0-1_arm64.deb 7573ae95e1e5dbadf11089a8497ce50eb93f50cf 8844 shasta-dbgsym_0.12.0-1_arm64.deb 7cdcf4717cdaf47196640c881bc70bc8f7ecfa20 15253 shasta_0.12.0-1_arm64.buildinfo 9bff84e5aa615969bc129f2b20da9f8d99ed1d24 614892 shasta_0.12.0-1_arm64.deb Checksums-Sha256: b3663c18d6933bbb1f353367bc3613c0c51b16c3460eab0ca2f790601112bf08 135820 python3-shasta-dbgsym_0.12.0-1_arm64.deb 317df22aab2c16c20eee54b09b97c36b90dabbc0e270b027434f1a43eb04b831 24032 python3-shasta-doc_0.12.0-1_all.deb 76fce9e54ab97a9ede90fd75a3fc5d32cd6847f432b767212324a3ed447f658c 1913208 python3-shasta_0.12.0-1_arm64.deb dd029e2751294c0a45108d9cf61924c4fda5845f5c4f115ad8aad186efa7013a 8844 shasta-dbgsym_0.12.0-1_arm64.deb 8fd39f0312394cf6c723ccbd6a40f43d8ec05df8489dd296df7e6bea29a150aa 15253 shasta_0.12.0-1_arm64.buildinfo 83da9040fa9601c02323f0469e5fd9a5ffaef7d01e9f38cd20d1e370be4fe83a 614892 shasta_0.12.0-1_arm64.deb Files: ceecc39a33733662f6eb95ad81fab4f4 135820 debug optional python3-shasta-dbgsym_0.12.0-1_arm64.deb b79ec8b5bd6cf986a900fba9c3a45053 24032 doc optional python3-shasta-doc_0.12.0-1_all.deb 56d6926686e83379f4ed4c0cca44f87d 1913208 python optional python3-shasta_0.12.0-1_arm64.deb dfc564daf99a7e6268f4bfc2854aebb8 8844 debug optional shasta-dbgsym_0.12.0-1_arm64.deb 0626ea424129f55d23112633444b8435 15253 science optional shasta_0.12.0-1_arm64.buildinfo e30f7e773c1fb8cd8c6fad47a7831922 614892 science optional shasta_0.12.0-1_arm64.deb Wed Jun 19 13:35:06 UTC 2024 I: diffoscope 271 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_22-17901.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/shasta_0.12.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/shasta_0.12.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/shasta_0.12.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/b1/shasta_0.12.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.zopMsMVp/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 abc.DotChangesFile ## main (total time: 0.390s) 0.390s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.046s) 0.046s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 722ms CPU time consumed: 723ms Wed Jun 19 13:35:08 UTC 2024 I: diffoscope 271 found no differences in the changes files, and a .buildinfo file also exists. Wed Jun 19 13:35:08 UTC 2024 I: shasta from unstable built successfully and reproducibly on arm64. Wed Jun 19 13:35:09 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Jun 19 13:35:09 UTC 2024 I: Submitting 16K b1/shasta_0.12.0-1_arm64.buildinfo.asc Wed Jun 19 13:35:11 UTC 2024 I: Submitting 16K b2/shasta_0.12.0-1_arm64.buildinfo.asc Wed Jun 19 13:35:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jun 19 13:35:12 UTC 2024 I: Done submitting .buildinfo files. Wed Jun 19 13:35:12 UTC 2024 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'