Thu May 9 05:08:24 UTC 2024 I: starting to build shasta/unstable/amd64 on jenkins on '2024-05-09 05:08' Thu May 9 05:08:24 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/6963/console.log Thu May 9 05:08:24 UTC 2024 I: Downloading source for unstable/shasta=0.11.1-5 --2024-05-09 05:08:25-- http://deb.debian.org/debian/pool/main/s/shasta/shasta_0.11.1-5.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_0.11.1-5.dsc’ 0K .. 100% 273M=0s 2024-05-09 05:08:25 (273 MB/s) - ‘shasta_0.11.1-5.dsc’ saved [2556/2556] Thu May 9 05:08:25 UTC 2024 I: shasta_0.11.1-5.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: 0.11.1-5 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust , Étienne Mollier Homepage: https://github.com/chanzuckerberg/shasta Standards-Version: 4.6.2 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: 372f39c1423a43164db29c55859397393a436744 3999058 shasta_0.11.1.orig.tar.gz 3b8f0af4fb42b8422b9bcf8bd7ec9dea7840e7f9 10812 shasta_0.11.1-5.debian.tar.xz Checksums-Sha256: 7fdf7cfd939f33a619773f5c6ca56e168b3e1cc77b9b7811a98ec06f6dd8ba9a 3999058 shasta_0.11.1.orig.tar.gz 30ea5aaece2b85383a63f70cbc466691539dae4f97596f0347da567438b526d9 10812 shasta_0.11.1-5.debian.tar.xz Files: c1ec064ed6fe3d2815d70bc3baa2e61f 3999058 shasta_0.11.1.orig.tar.gz b39edce37da1e839159a6cf81bcb9335 10812 shasta_0.11.1-5.debian.tar.xz Dgit: f493a18b33a81eef8875bda2295b0963e5c3164c debian archive/debian/0.11.1-5 https://git.dgit.debian.org/shasta -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmY723MUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp7WhAAuY9zKesQNGrpDu1+wjJBazYUilrC h/3es0PPFNHF9Q8RkwO5Hpx1/RyLkoB06TzMwtu5X7u2NBAe6DQuBYaeYIlDKAzR h6HWXl6Gnnx1zDLlsoVHlreuaWrxbtg5dwTV36dLy2snmwIoUUO49LgOs3H9makD 3BZjef+01BPCwW8VEIRCZAtA2l7QcGw+ntAYieZWlsVQ4/T3K1e+rDmIcrzFudW+ YQG5nZne/M6+CAjy4OT1/o/gjfq8rASGue0DsiOM0YN4SOlVEuK8yyfFI9EU2obS zt9x3aQTObriCgQXoPdTdCUAA775faK4D5numozx+sLY6lsz81tOAU5jEnproqSf COEDwLEbWyUqR4WZcbO5bIF4MG+DeH2DRKa/2Of+ZGJgiOpBnR5zAMx1DYH3t4CS Tj4E/qNHZ1SwmyX7KKQBBJDdqJMXUubpNURohMR4qKgli7t8xQR72fxpNlX2e69n Vn54givol86+oSC4r83eTEUYnjOg30Dv6VxKBOC9kh1VCQaMUQg9s1/gTMW//cbL TA2qW2pgxUR87iPphkHGRHFYmVRL3oG0MQjIRBLS3zwtSVzE2V6+VzffwIUoKKIv GS7XgIw4pwpWhNNlPo4IA0ScEwAriWnJSDJOEbcJgwiUzFRk02hX3LtR8ZZp/WE6 Bo7K2GjfjJva40g= =l21Q -----END PGP SIGNATURE----- Thu May 9 05:08:25 UTC 2024 I: Checking whether the package is not for us Thu May 9 05:08:25 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu May 9 05:08:25 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu May 9 05:21:13 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 8 17:08:28 -12 2024 I: pbuilder-time-stamp: 1715231308 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_0.11.1-5.dsc] I: copying [./shasta_0.11.1.orig.tar.gz] I: copying [./shasta_0.11.1-5.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 8 20:07:15 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_0.11.1-5.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.11.1 dpkg-source: info: unpacking shasta_0.11.1.orig.tar.gz dpkg-source: info: unpacking shasta_0.11.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying gcc-13-bis.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1051948/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e0ea4a8fa3b84721ae5d71de0c0161a5' 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='1051948' 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.gxEzZ7q4/pbuilderrc_Qve5 --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.gxEzZ7q4/b1 --logfile b1/build.log shasta_0.11.1-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 7 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1051948/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: amd64 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, libcpu-features-dev, 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 ... 19699 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 libcpu-features-dev; however: Package libcpu-features-dev 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-x86-64-linux-gnu{a} gfortran-x86-64-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} libcpu-features-dev{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} 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} libpsm-infinipath1{a} libpsm2-2{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} libsub-override-perl{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-six{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, 298 newly installed, 0 to remove and 0 not upgraded. Need to get 216 MB of archives. After unpacking 1142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 70 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get: 87 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7 [1280 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:13.2.0-7 [1440 B] Get: 90 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-2.1+b1 [235 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 111 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-2.1+b1 [239 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-2.1+b1 [244 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83.0 amd64 1.83.0-2.1+b1 [259 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83-dev amd64 1.83.0-2.1+b1 [264 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 117 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-2.1+b1 [230 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-2.1+b1 [332 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-2.1+b1 [372 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-2.1+b1 [239 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-2.1+b1 [230 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-2.1+b1 [231 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-2.1+b1 [269 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-2.1+b1 [277 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83.0 amd64 1.83.0-2.1+b1 [231 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83-dev amd64 1.83.0-2.1+b1 [232 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.83-dev amd64 1.83.0-2.1+b1 [230 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 135 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-2.1+b1 [280 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-2.1+b1 [295 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83.0 amd64 1.83.0-2.1+b1 [253 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83-dev amd64 1.83.0-2.1+b1 [264 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 140 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 141 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-2.1+b1 [358 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-2.1+b1 [325 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-2.1+b1 [342 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-2.1+b1 [466 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-2.1+b1 [537 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-2.1+b1 [383 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 149 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83.0 amd64 1.83.0-2.1+b1 [271 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-2.1+b1 [279 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-2.1+b1 [283 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 174 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-2.1+b1 [261 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 176 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83.0 amd64 1.83.0-2.1+b1 [354 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83-dev amd64 1.83.0-2.1+b1 [369 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83.0 amd64 1.83.0-2.1+b1 [464 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83-dev amd64 1.83.0-2.1+b1 [548 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 182 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83.0 amd64 1.83.0-2.1+b1 [700 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83-dev amd64 1.83.0-2.1+b1 [870 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 185 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83.0 amd64 1.83.0-2.1+b1 [506 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83-dev amd64 1.83.0-2.1+b1 [548 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 188 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 50.0-2+b1 [642 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [181 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [107 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [61.1 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-8.1+b3 [305 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.15 [3152 B] Get: 207 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83-dev amd64 1.83.0-2.1+b1 [289 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 209 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-2.1+b1 [351 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.15 [2408 B] Get: 211 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-2.1+b1 [435 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-2.1+b1 [239 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 214 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 217 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83.0 amd64 1.83.0-2.1+b1 [248 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83-dev amd64 1.83.0-2.1+b1 [253 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 220 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1+b1 [345 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-2.1+b1 [373 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-2.1+b1 [379 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 233 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83.0 amd64 1.83.0-2.1+b1 [238 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83-dev amd64 1.83.0-2.1+b1 [240 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 236 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 237 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 238 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-2.1+b1 [280 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-2.1+b1 [245 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 241 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 242 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 243 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 244 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 247 http://deb.debian.org/debian unstable/main amd64 libboost1.83-tools-dev amd64 1.83.0-2.1+b1 [1500 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 249 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-2.1+b1 [245 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-2.1+b1 [248 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83.0 amd64 1.83.0-2.1+b1 [336 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83-dev amd64 1.83.0-2.1+b1 [422 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 255 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83.0 amd64 1.83.0-2.1+b1 [434 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83-dev amd64 1.83.0-2.1+b1 [483 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 258 http://deb.debian.org/debian unstable/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 259 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libcpu-features-dev amd64 0.9.0-1+b1 [22.0 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-1 [70.3 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libspoa-dev amd64 4.1.4-1 [9400 B] Get: 274 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 276 http://deb.debian.org/debian unstable/main amd64 patchelf amd64 0.18.0-1.1 [97.1 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.11.1-2 [191 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-roman all 3.3-3 [9880 B] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.6-2 [37.0 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.11.1-2 [201 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.2.6-6 [702 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.2.6-6 [552 kB] Fetched 216 MB in 5s (42.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.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:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.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:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... 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Setting up libboost-all-dev (1.83.0.2+b2) ... Processing triggers for libc-bin (2.38-8) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shasta-0.11.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.11.1-5_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.11.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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-0.11.1' dh_auto_configure -- -DBUILD_ID=0.11.1 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-x86_64-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/x86_64-linux-gnu -DBUILD_ID=0.11.1 -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 x86_64 -- 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: 0.11.1 -- Configuring done (2.2s) -- Generating done (0.2s) 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-0.11.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.11.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1' dh_auto_build cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.11.1 -B/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.11.1 /build/reproducible-path/shasta-0.11.1/staticLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.11.1 /build/reproducible-path/shasta-0.11.1/dynamicLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AlignmentGraph.cpp [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Align4.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssembledSegment.cpp [ 4%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAlign.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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 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/build/reproducible-path/shasta-0.11.1/src/AssembledSegment.cpp cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Assembler.cpp cd 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign.cpp cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAlign4.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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 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-o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign3.cpp cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAlignmentCandidates.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAlign4.cpp [ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAnalyzePaths.cpp /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/string:42, from /build/reproducible-path/shasta-0.11.1/src/string.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.11.1/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.11.1/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/string:42, from /build/reproducible-path/shasta-0.11.1/src/string.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.11.1/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.11.1/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerAlignmentCandidates.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAssemblyGraph.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAssemblyGraph2.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerAlignmentGraph.cpp /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 13%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerCompressedAssemblyGraph.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerHttpServer.cpp [ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerInducedAlignments.cpp [ 21%] Building CXX object 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerKmers.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerKmers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerKmers.cpp.o.d -o 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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-0.11.1/src/AssemblerHttpServer-Alignments.cpp [ 23%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerLowHash.cpp [ 23%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerMarkerConnectivityGraph.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerHttpServer-AssemblyGraph.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerMarkerGraph.cpp In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/shasta-0.11.1/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.11.1/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.11.1/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1623:53: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.11.1/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1668:57: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerMarkerGraphEdges.cpp [ 26%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerMarkers.cpp [ 26%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerMode3.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerOptions.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerHttpServer-MarkerGraph.cpp [ 28%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerReadGraph.cpp In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/shasta-0.11.1/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.11.1/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.11.1/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1623:53: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.11.1/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblerAssemblyGraph.cpp:1668:57: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerReadGraph2.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblerReads.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblyGraph.cpp [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerHttpServer-Mode3.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblyGraph2.cpp [ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblyPathGraph.cpp [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerHttpServer-ReadGraph.cpp [ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/AssemblyPathGraph2.cpp [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. 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-DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LowHash0.cpp [ 78%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS 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-DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MarkerFinder.cpp [ 79%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MarkerGraph.cpp [ 79%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MedianConsensusCaller.cpp [ 80%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MemoryMappedAllocator.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.hpp:29, from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [ 80%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MemoryMappedVector.cpp [ 81%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MultithreadedObject.cpp [ 81%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MurmurHash2.cpp [ 82%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PeakFinder.cpp [ 82%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PhasingGraph.cpp [ 83%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PngImage.cpp [ 83%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PythonModule.cpp [ 84%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ReadGraph.cpp [ 84%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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/build/reproducible-path/shasta-0.11.1/src/mode3-Detangler.cpp [ 93%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp [ 94%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp [ 94%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-PathGraph.cpp [ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3.cpp [ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/performanceLog.cpp [ 96%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/platformDependent.cpp [ 96%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/runCommandWithTimeout.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/shastaLapack.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/testSpoa.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/testSubsetGraph.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/timestamp.cpp [ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -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-0.11.1/src/touchMemory.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.hpp:29, from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [100%] Linking CXX static library shasta.a cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 /usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.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/AssemblerKmers.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/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o /usr/bin/ranlib shasta.a make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' [100%] Built target shastaStaticLibrary [100%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o 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/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.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/LocalMarkerGraph-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.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/LowHash1.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/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/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lpthread -lz -lspoa -llapack -lblas -lpython3.11 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-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-0.11.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.11.1 /build/reproducible-path/shasta-0.11.1/dynamicExecutable /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' [100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -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-0.11.1/srcMain/main.cpp [100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-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-0.11.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.11 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; 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-0.11.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/shasta-0.11.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.11.1 -B/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: 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/build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/conf.py -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/index.rst -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/Makefile -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/shasta.so -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/README -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/Introduction.html -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/QuickStart.html -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/SupportedPlatforms.html -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/ChooseMemoryOptions.html -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/style.css -- Installing: /build/reproducible-path/shasta-0.11.1/debian/tmp/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/./shasta-install/docs/index.html make[1]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1' 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-0.11.1' 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-x86_64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1' patchelf \ --set-soname shasta.cpython-311-x86_64-linux-gnu.so \ /build/reproducible-path/shasta-0.11.1/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-x86_64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.11.1' 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-0.11.1' # 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-0.11.1 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.11.1' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-311-x86_64-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: 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-0.11.1' # 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-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-311-x86_64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.11.1' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.11.1-5_amd64.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.11.1-5_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.11.1-5_amd64.deb'. dpkg-deb: building package 'shasta' in '../shasta_0.11.1-5_amd64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.11.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.11.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.11.1-5_amd64.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: not including original 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/1051948 and its subdirectories I: Current time: Wed May 8 17:21:13 -12 2024 I: pbuilder-time-stamp: 1715232073 Thu May 9 05:21:14 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu May 9 05:21:14 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu May 9 05:24:41 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu May 9 05:24:41 UTC 2024 I: shasta_0.11.1-5_amd64.changes: Format: 1.8 Date: Wed, 08 May 2024 22:02:57 +0200 Source: shasta Binary: python3-shasta python3-shasta-dbgsym python3-shasta-doc shasta shasta-dbgsym Architecture: amd64 all Version: 0.11.1-5 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) Closes: 1069370 Changes: shasta (0.11.1-5) unstable; urgency=medium . * d/rules: meddle with RPATH only after dh_shlibdeps. (Closes: #1069370) Checksums-Sha1: d616d011a8ba5f7aafd877da92b75fd1838770f5 115592 python3-shasta-dbgsym_0.11.1-5_amd64.deb b24dbe7c94bf8ec5f8218baabaac2d4e780aecaf 24740 python3-shasta-doc_0.11.1-5_all.deb 13b295a9325d0d5f1626d37565c635fce1026516 2111856 python3-shasta_0.11.1-5_amd64.deb 70c9cf865d977a08a811f8f1c036a3430b925efc 8336 shasta-dbgsym_0.11.1-5_amd64.deb d59730c2ec5fdc4b6c1a8205d433e4ebf6fac253 15874 shasta_0.11.1-5_amd64.buildinfo 0caa35afa9de8932caad403f9a392cf0d8ac0600 623352 shasta_0.11.1-5_amd64.deb Checksums-Sha256: d775ebeb49f52e1cd0aa8e3ab3a880dd2830bccab9316eddfccb7c30629a9719 115592 python3-shasta-dbgsym_0.11.1-5_amd64.deb 6afc895a8e29bfea42d0318771865e31fe145204143b2eca3f01c024765687ac 24740 python3-shasta-doc_0.11.1-5_all.deb f7289f98bdf388844866b5fe0496eba681b8824df29e357bbb0c959713cf1a63 2111856 python3-shasta_0.11.1-5_amd64.deb 5472a7a148d6141e8f63c26427925252eafbf70a1cbae8f3f723760af5bf8300 8336 shasta-dbgsym_0.11.1-5_amd64.deb cd21cd9e6c7749af2f125398a7fa34da5547074bead64e64c41a4f26ccaf231e 15874 shasta_0.11.1-5_amd64.buildinfo ba93784b067835aa0b0f45decaa75cf6ff5f64e818a862adccb89fdff5d4b60c 623352 shasta_0.11.1-5_amd64.deb Files: adb0e2d0b2f5e81da172deafab792459 115592 debug optional python3-shasta-dbgsym_0.11.1-5_amd64.deb 87aedd4f4dfb7013b4ae18cd43a94cc2 24740 doc optional python3-shasta-doc_0.11.1-5_all.deb ac40767f818e77d1f9bacbe9c33082db 2111856 python optional python3-shasta_0.11.1-5_amd64.deb 6b19249da5fc4b6bf76b0904e90ff48a 8336 debug optional shasta-dbgsym_0.11.1-5_amd64.deb 90afb4eccac2049f4ba20ad045833f4a 15874 science optional shasta_0.11.1-5_amd64.buildinfo a3dafea5141267fe3ac2b7b6891343db 623352 science optional shasta_0.11.1-5_amd64.deb Thu May 9 05:24:43 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_13-6963.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gxEzZ7q4/shasta_0.11.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gxEzZ7q4/shasta_0.11.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gxEzZ7q4/shasta_0.11.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gxEzZ7q4/b1/shasta_0.11.1-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.gxEzZ7q4/b2/shasta_0.11.1-5_amd64.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: 0.397s) 0.397s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.049s) 0.049s 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: 734ms CPU time consumed: 732ms Thu May 9 05:24:45 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 05:24:45 UTC 2024 I: shasta from unstable built successfully and reproducibly on amd64. Thu May 9 05:24:46 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 05:24:46 UTC 2024 I: Submitting 20K b1/shasta_0.11.1-5_amd64.buildinfo.asc Thu May 9 05:24:47 UTC 2024 I: Submitting 20K b2/shasta_0.11.1-5_amd64.buildinfo.asc Thu May 9 05:24:48 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 05:24:48 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 05:24:48 UTC 2024 I: Removing signed shasta_0.11.1-5_amd64.buildinfo.asc files: removed './b1/shasta_0.11.1-5_amd64.buildinfo.asc' removed './b2/shasta_0.11.1-5_amd64.buildinfo.asc'