Running as unit: rb-build-arm64_4-37435.service ==================================================================================== Fri Sep 27 17:41:06 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_4) on jenkins, called using "codethink02-arm64 codethink01-arm64" as arguments. Fri Sep 27 17:41:06 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-CrTXH3ni" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 17:41:06 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 17:41:06 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-WpwmXJ' Fri Sep 27 17:41:06 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Sep 27 17:41:06 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-P6pod9' ok, let's check if consensuscore is building anywhere yet… ok, consensuscore is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of consensuscore in unstable on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Fri Sep 27 17:41:08 UTC 2024 I: starting to build consensuscore/unstable/arm64 on jenkins on '2024-09-27 17:41' Fri Sep 27 17:41:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/37435/console.log 1727458868 arm64 unstable consensuscore Fri Sep 27 17:41:08 UTC 2024 I: Downloading source for unstable/consensuscore=1.1.1+dfsg-7 --2024-09-27 17:41:09-- http://deb.debian.org/debian/pool/main/c/consensuscore/consensuscore_1.1.1%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2328 (2.3K) [text/prs.lines.tag] Saving to: ‘consensuscore_1.1.1+dfsg-7.dsc’ 0K .. 100% 307M=0s 2024-09-27 17:41:09 (307 MB/s) - ‘consensuscore_1.1.1+dfsg-7.dsc’ saved [2328/2328] --2024-09-27 17:41:09-- http://deb.debian.org/debian/pool/main/c/consensuscore/consensuscore_1.1.1%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2328 (2.3K) [text/prs.lines.tag] Saving to: ‘consensuscore_1.1.1+dfsg-7.dsc’ 0K .. 100% 307M=0s 2024-09-27 17:41:09 (307 MB/s) - ‘consensuscore_1.1.1+dfsg-7.dsc’ saved [2328/2328] Fri Sep 27 17:41:09 UTC 2024 I: consensuscore_1.1.1+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: consensuscore Binary: libconsensuscore-dev, python3-pbconsensuscore Architecture: any Version: 1.1.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/ConsensusCore Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/consensuscore Vcs-Git: https://salsa.debian.org/med-team/consensuscore.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), architecture-is-64-bit [!i386], architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev Package-List: libconsensuscore-dev deb libdevel optional arch=any python3-pbconsensuscore deb python optional arch=any Checksums-Sha1: 06118ce273ef10180336ab071fd86dc60aea7168 363936 consensuscore_1.1.1+dfsg.orig.tar.xz 411978f41eeb4990333b4d58ef5f0774e79e8a89 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz Checksums-Sha256: 47865e3769e2d6647003f70ffce68f8a5b2f69a6ae04ff27d106b3ec84660d82 363936 consensuscore_1.1.1+dfsg.orig.tar.xz a3a14e0f188d22d3e7d77cf5f7f0d1cf1575a3bc71c04336bc2392f1c5889057 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz Files: 17991299008d1c01e25ce3984b7fe7bd 363936 consensuscore_1.1.1+dfsg.orig.tar.xz f424059779de3d65f09a18cd2d9b316e 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYAT9YACgkQPCZ2P2xn 5uLqtxAAv/8Q251QRDNHDdqMMcx8g8pSgdWkI3CtNY4XoZ1rSJEFBLxaSt0pZf60 l2bMZHGH7SohyqrWnXsrsUwByyQpvMC7rgstBjM7N8TFT3O8Q4G2GnugHixFvMet XUr5BlGb8XnNCKy8Bjh6JDJrlv1Ipnvo+u1GEhiW4Jb5QAteecxq1Zo9hFlacF0Y +XYvu4T4JzkAFIxTo1AqtCtj5yZU0kukc8pR4qQaX0gp00EvHwejZT2oa32w893S y4davnj8VSy6VSZZpjp1SWN4t/uG9LjsxU5Hw7vnSHmk+HYEMUSuugl5wCf/7g99 C9uFrV62DeMr5qp4XmRQqy0AmmvFidJeSh2NbEzBbHytSRIHJjjDckuZBcqn9JlL 5JFZQFjOpjCShSOTePMZ6unbHPYCq9cQAk715bmRpktr5ZzzBLAAiWZ7kFY7rpka fSfd52Uy71bYnNUSwGkjXA+lM7fL0cvTUdW2InUsYNU9/BBvhXuipc0VO1tzbyYO Zv6X3lVW5YjiS83od/DLKPdOxOtbBFVVYBN8LQywP2/v9495OnXJQvezpUALr1W5 WvHU8wRFU2JOBakTacVOGkcCDOvfQnWtT5owQzyEpvBTebgaRjYQpduhLyNFihi4 4j0DH0ds42WZEyKKEOMCBhwD0AVE1MiRzbIn636zrYGlqJ0ZyPI= =uv0b -----END PGP SIGNATURE----- Fri Sep 27 17:41:09 UTC 2024 I: Checking whether the package is not for us Fri Sep 27 17:41:09 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Sep 27 17:41:09 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Sep 27 17:41:09 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 17:41:09 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-irm59f' ==================================================================================== Fri Sep 27 17:41:10 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 consensuscore unstable /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3 1.1.1+dfsg-7" as arguments. Fri Sep 27 17:41:10 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-zbjjX2ua" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 17:41:11 UTC 2024 I: Downloading source for unstable/consensuscore=1.1.1+dfsg-7 Reading package lists... NOTICE: 'consensuscore' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/consensuscore.git Please use: git clone https://salsa.debian.org/med-team/consensuscore.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 376 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (dsc) [2328 B] Get:2 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (tar) [364 kB] Get:3 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (diff) [10.1 kB] Fetched 376 kB in 0s (3909 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'consensuscore' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/consensuscore.git Please use: git clone https://salsa.debian.org/med-team/consensuscore.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 376 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (dsc) [2328 B] Get:2 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (tar) [364 kB] Get:3 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (diff) [10.1 kB] Fetched 376 kB in 0s (3909 kB/s) Download complete and in download only mode ============================================================================= Building consensuscore in unstable on arm64 on codethink02-arm64 now. Date: Fri Sep 27 18:41:11 BST 2024 Date UTC: Fri Sep 27 17:41:11 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 27 05:41:11 -12 2024 I: pbuilder-time-stamp: 1727458871 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 [consensuscore_1.1.1+dfsg-7.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 24 16:07:50 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying check_boost_version.patch dpkg-source: info: applying sequence_setuptools.patch dpkg-source: info: applying portable_simd.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6d5fa6ab37db45d3880e73d9bd8db887' 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='1096911' 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.sQlON7a3/pbuilderrc_uOJf --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.sQlON7a3/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libsimde-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 54.4 MB of archives. After unpacking 359 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 34 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30 [25.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240824 [109 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-5 [361 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.6-1 [1981 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.6-1 [4782 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 78 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 79 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 81 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.6-1 [506 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] Fetched 54.4 MB in 0s (208 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20217 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21289 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. 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Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../38-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../39-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../40-python3-zipp_3.20.2-1_all.deb ... Unpacking python3-zipp (3.20.2-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../41-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../42-dh-python_6.20240824_all.deb ... Unpacking dh-python (6.20240824) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../43-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../44-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../45-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../46-libexpat1-dev_2.6.3-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.3-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../47-libgfortran5_14.2.0-5_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-5) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../48-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. 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Unpacking libpython3.12-dev:arm64 (3.12.6-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../55-libpython3-dev_3.12.6-1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.12.6-1) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../56-libpython3-all-dev_3.12.6-1_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.12.6-1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../57-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../58-python3-all_3.12.6-1_arm64.deb ... Unpacking python3-all (3.12.6-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../59-python3.12-dev_3.12.6-1_arm64.deb ... Unpacking python3.12-dev (3.12.6-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../60-python3-dev_3.12.6-1_arm64.deb ... Unpacking python3-dev (3.12.6-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../61-python3-all-dev_3.12.6-1_arm64.deb ... Unpacking python3-all-dev (3.12.6-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../62-python3-numpy_1%3a1.26.4+ds-11_arm64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) ... Selecting previously unselected package swig. Preparing to unpack .../63-swig_4.2.1-1_arm64.deb ... Unpacking swig (4.2.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libboost1.83-dev:arm64 (1.83.0-3.2) ... Setting up swig (4.2.1-1) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:arm64 (0.2.3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 27 17:41:49 UTC 2024. Universal Time is now: Fri Sep 27 17:41:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.3-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... 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Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libpython3.12t64:arm64 (3.12.6-1) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:arm64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3.12-dev (3.12.6-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up libpython3-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:arm64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-3) ... 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/consensuscore-1.1.1+dfsg/ && 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 > ../consensuscore_1.1.1+dfsg-7_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SseRecursor.hpp:5, from src/C++/Quiver/SseRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from src/C++/Quiver/SimpleRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from src/C++/Quiver/ReadScorer.cpp:7: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from src/C++/Quiver/detail/RecursorBase.cpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QuiverConsensus.hpp:6, from src/C++/Quiver/QuiverConsensus.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from src/C++/Quiver/MutationScorer.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here 190 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:191:16: required from here 191 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:192:16: required from here 192 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:193:16: required from here 193 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:194:16: required from here 194 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:195:16: required from here 195 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here 196 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from src/C++/Quiver/MultiReadMutationScorer.cpp:5: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from src/C++/Edna/EdnaCounts.cpp:4: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o touch /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp:5: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (0 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (1 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (1 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (1 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (3 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (2 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (2 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (1 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (8 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (14 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (19 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (18 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/0 (84 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (25 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (25 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (26 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/1 (99 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (32 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (48 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (73 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (19 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (19 ms) [----------] 5 tests from RecursorFuzzTest/2 (203 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (58 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (54 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (54 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (12 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (11 ms) [----------] 5 tests from RecursorFuzzTest/3 (203 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (33 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (34 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (39 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (25 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (3 ms) [----------] 5 tests from QvEvaluatorTest (136 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (1 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (26 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (552 ms) [----------] 8 tests from PoaConsensus (580 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (9 ms) [----------] 2 tests from AffineAlignmentTests (9 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (0 ms) [----------] 1 test from LinearAlignmentTests (0 ms total) [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (1 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (0 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (2 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (2 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (2 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (2 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (1 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (1 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (2 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (1 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) [----------] 11 tests from MatrixTest/0 (2 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (5 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (6 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (0 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (1354 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore.py to ConsensusCore.cpython-312.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.egg-info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' adding license file 'LICENSES' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' find debian -name meson.build -delete make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 fs:418: renaming _ConsensusCore.so to _ConsensusCore.cpython-312-aarch64-linux-gnu.so debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/1096911 and its subdirectories I: Current time: Fri Sep 27 05:46:51 -12 2024 I: pbuilder-time-stamp: 1727459211 Fri Sep 27 17:46:51 UTC 2024 I: Signing ./b1/consensuscore_1.1.1+dfsg-7_arm64.buildinfo as consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc Fri Sep 27 17:46:51 UTC 2024 I: Signed ./b1/consensuscore_1.1.1+dfsg-7_arm64.buildinfo as ./b1/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc Fri Sep 27 17:46:51 UTC 2024 - build #1 for consensuscore/unstable/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Fri Sep 27 17:46:51 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-zbjjX2ua, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 17:46 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 17:41 b2 -rw-r--r-- 1 jenkins jenkins 2328 Mar 24 2024 consensuscore_1.1.1+dfsg-7.dsc -rw------- 1 jenkins jenkins 3506 Sep 27 17:41 rbuildlog.itqJgLf /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b1: total 10268 -rw-r--r-- 1 jenkins jenkins 218482 Sep 27 17:46 build.log -rw-r--r-- 1 jenkins jenkins 10136 Sep 27 17:46 consensuscore_1.1.1+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2328 Sep 27 17:46 consensuscore_1.1.1+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 7136 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8018 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2054 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1371 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 475924 Sep 27 17:46 libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9124872 Sep 27 17:46 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 646000 Sep 27 17:46 python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2: total 0 Fri Sep 27 17:46:52 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 27 05:41:11 -12 2024 I: pbuilder-time-stamp: 1727458871 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 [consensuscore_1.1.1+dfsg-7.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 24 16:07:50 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying check_boost_version.patch dpkg-source: info: applying sequence_setuptools.patch dpkg-source: info: applying portable_simd.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6d5fa6ab37db45d3880e73d9bd8db887' 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='1096911' 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.sQlON7a3/pbuilderrc_uOJf --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.sQlON7a3/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libsimde-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 54.4 MB of archives. After unpacking 359 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 34 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30 [25.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240824 [109 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-5 [361 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.6-1 [1981 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.6-1 [4782 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 78 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 79 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 81 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.6-1 [506 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] Fetched 54.4 MB in 0s (208 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20217 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21289 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../11-architecture-properties_0.2.3_arm64.deb ... Unpacking architecture-properties:arm64 (0.2.3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... 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Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 27 17:41:49 UTC 2024. Universal Time is now: Fri Sep 27 17:41:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.3-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... 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Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... 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Processing triggers for libc-bin (2.40-3) ... 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/consensuscore-1.1.1+dfsg/ && 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 > ../consensuscore_1.1.1+dfsg-7_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SseRecursor.hpp:5, from src/C++/Quiver/SseRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from src/C++/Quiver/SimpleRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from src/C++/Quiver/ReadScorer.cpp:7: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from src/C++/Quiver/detail/RecursorBase.cpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QuiverConsensus.hpp:6, from src/C++/Quiver/QuiverConsensus.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from src/C++/Quiver/MutationScorer.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here 190 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:191:16: required from here 191 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:192:16: required from here 192 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:193:16: required from here 193 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:194:16: required from here 194 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:195:16: required from here 195 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here 196 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from src/C++/Quiver/MultiReadMutationScorer.cpp:5: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from src/C++/Edna/EdnaCounts.cpp:4: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o touch /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp:5: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (0 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (1 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (1 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (1 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (3 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (2 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (2 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (1 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (8 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (14 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (19 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (18 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/0 (84 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (25 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (25 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (26 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/1 (99 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (32 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (48 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (73 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (19 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (19 ms) [----------] 5 tests from RecursorFuzzTest/2 (203 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (58 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (54 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (54 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (12 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (11 ms) [----------] 5 tests from RecursorFuzzTest/3 (203 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (33 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (34 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (39 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (25 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (3 ms) [----------] 5 tests from QvEvaluatorTest (136 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (1 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (26 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (552 ms) [----------] 8 tests from PoaConsensus (580 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (9 ms) [----------] 2 tests from AffineAlignmentTests (9 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (0 ms) [----------] 1 test from LinearAlignmentTests (0 ms total) [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (1 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (0 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (2 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (2 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (2 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (2 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (1 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (1 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (2 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (1 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) [----------] 11 tests from MatrixTest/0 (2 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (5 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (6 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (0 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (1354 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore.py to ConsensusCore.cpython-312.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.egg-info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' adding license file 'LICENSES' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' find debian -name meson.build -delete make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 fs:418: renaming _ConsensusCore.so to _ConsensusCore.cpython-312-aarch64-linux-gnu.so debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/1096911 and its subdirectories I: Current time: Fri Sep 27 05:46:51 -12 2024 I: pbuilder-time-stamp: 1727459211 Fri Sep 27 17:46:53 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Fri Sep 27 17:46:53 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Fri Sep 27 17:46:53 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Sep 27 17:46:53 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-S7bsFn' ==================================================================================== Fri Oct 31 00:09:53 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 consensuscore unstable /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3 1.1.1+dfsg-7" as arguments. Fri Oct 31 00:09:53 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-o0pAvtTM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 00:09:53 UTC 2025 I: Downloading source for unstable/consensuscore=1.1.1+dfsg-7 Reading package lists... NOTICE: 'consensuscore' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/consensuscore.git Please use: git clone https://salsa.debian.org/med-team/consensuscore.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 376 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (dsc) [2328 B] Get:2 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (tar) [364 kB] Get:3 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (diff) [10.1 kB] Fetched 376 kB in 0s (18.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'consensuscore' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/consensuscore.git Please use: git clone https://salsa.debian.org/med-team/consensuscore.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 376 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (dsc) [2328 B] Get:2 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (tar) [364 kB] Get:3 http://deb.debian.org/debian unstable/main consensuscore 1.1.1+dfsg-7 (diff) [10.1 kB] Fetched 376 kB in 0s (18.4 MB/s) Download complete and in download only mode ============================================================================= Re-Building consensuscore in unstable on arm64 on codethink01-arm64 now. Date: Fri Oct 31 00:09:53 GMT 2025 Date UTC: Fri Oct 31 00:09:53 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/pbuilderrc_mKIh + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' consensuscore = debian-installer -o consensuscore = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' consensuscore = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/pbuilderrc_mKIh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-7.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 14:09:53 +14 2025 I: pbuilder-time-stamp: 1761869393 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 [consensuscore_1.1.1+dfsg-7.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 24 16:07:50 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying check_boost_version.patch dpkg-source: info: applying sequence_setuptools.patch dpkg-source: info: applying portable_simd.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 31 00:10 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=7c6352e8ef7a42f9bd0b0babd9211011 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2261779 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/pbuilderrc_mKIh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-7.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libsimde-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 54.4 MB of archives. After unpacking 359 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 34 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30 [25.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240824 [109 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-5 [361 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.6-1 [1981 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.6-1 [4782 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 78 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 79 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 81 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.6-1 [506 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] Fetched 54.4 MB in 0s (191 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20217 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21289 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../11-architecture-properties_0.2.3_arm64.deb ... Unpacking architecture-properties:arm64 (0.2.3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package dh-exec. Preparing to unpack .../31-dh-exec_0.30_arm64.deb ... Unpacking dh-exec (0.30) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../32-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../33-python3-more-itertools_10.4.0-1_all.deb ... Unpacking python3-more-itertools (10.4.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../34-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../35-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../36-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../37-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../38-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../39-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../40-python3-zipp_3.20.2-1_all.deb ... Unpacking python3-zipp (3.20.2-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../41-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../42-dh-python_6.20240824_all.deb ... Unpacking dh-python (6.20240824) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../43-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../44-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../45-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../46-libexpat1-dev_2.6.3-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.3-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../47-libgfortran5_14.2.0-5_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-5) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../48-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. 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Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/2261779/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-7_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SseRecursor.hpp:5, from src/C++/Quiver/SseRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from src/C++/Quiver/SimpleRecursor.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, from src/C++/Quiver/detail/RecursorBase.cpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from src/C++/Quiver/ReadScorer.cpp:7: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QuiverConsensus.hpp:6, from src/C++/Quiver/QuiverConsensus.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from src/C++/Quiver/MutationScorer.cpp:3: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here 190 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:191:16: required from here 191 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:192:16: required from here 192 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:193:16: required from here 193 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:194:16: required from here 194 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:195:16: required from here 195 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here 196 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:6, from src/C++/Quiver/MultiReadMutationScorer.cpp:5: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse3.h:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from src/C++/Edna/EdnaCounts.cpp:4: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:490:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 490 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf cos_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:582:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 582 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:591:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 591 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:592:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 592 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:595:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 595 | emm2 = _mm_sub_epi32(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:598:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 598 | emm0 = _mm_andnot_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:705:46: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 705 | sign_bit_sin = _mm_and_ps(sign_bit_sin, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:715:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 715 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:716:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 716 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:722:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 722 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:727:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 727 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:778:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 778 | emm4 = _mm_sub_epi32(emm4, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o touch /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp:5: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (1 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (1 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (2 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (3 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (4 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (4 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (5 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (4 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (25 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (19 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (17 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (15 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (13 ms) [----------] 5 tests from RecursorFuzzTest/0 (89 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (27 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (25 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (26 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/1 (101 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (32 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (32 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (36 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (11 ms) [----------] 5 tests from RecursorFuzzTest/2 (122 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (29 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (29 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (29 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (10 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (11 ms) [----------] 5 tests from RecursorFuzzTest/3 (108 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (33 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (33 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (39 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (25 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (3 ms) [----------] 5 tests from QvEvaluatorTest (133 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (0 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (0 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: line 1: dot: command not found [ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (479 ms) [----------] 8 tests from PoaConsensus (487 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (7 ms) [----------] 2 tests from AffineAlignmentTests (7 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (0 ms) [----------] 1 test from LinearAlignmentTests (0 ms total) [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (0 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (1 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (2 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (0 ms) [----------] 8 tests from MutationScorerTest/1 (1 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (0 ms) [----------] 8 tests from MutationScorerTest/2 (1 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (2 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (1 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (1 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (0 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (2 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (1 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) [----------] 11 tests from MatrixTest/0 (1 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (6 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (6 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (0 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (1078 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore.py to ConsensusCore.cpython-312.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.egg-info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' adding license file 'LICENSES' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' find debian -name meson.build -delete make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 fs:418: renaming _ConsensusCore.so to _ConsensusCore.cpython-312-aarch64-linux-gnu.so debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2261779 and its subdirectories I: Current time: Fri Oct 31 14:14:22 +14 2025 I: pbuilder-time-stamp: 1761869662 + false + set +x Fri Oct 31 00:14:22 UTC 2025 I: Signing ./b2/consensuscore_1.1.1+dfsg-7_arm64.buildinfo as consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc Fri Oct 31 00:14:22 UTC 2025 I: Signed ./b2/consensuscore_1.1.1+dfsg-7_arm64.buildinfo as ./b2/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc Fri Oct 31 00:14:22 UTC 2025 - build #2 for consensuscore/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Fri Oct 31 00:14:22 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-o0pAvtTM, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3: total 236 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 17:46 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 17:51 b2 -rw-r--r-- 1 jenkins jenkins 2328 Mar 24 2024 consensuscore_1.1.1+dfsg-7.dsc -rw------- 1 jenkins jenkins 222289 Sep 27 17:46 rbuildlog.itqJgLf /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b1: total 10296 -rw-r--r-- 1 jenkins jenkins 218482 Sep 27 17:46 build.log -rw-r--r-- 1 jenkins jenkins 10136 Sep 27 17:46 consensuscore_1.1.1+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2328 Sep 27 17:46 consensuscore_1.1.1+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 7136 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8018 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2054 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1371 Sep 27 17:46 consensuscore_1.1.1+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 475924 Sep 27 17:46 libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9124872 Sep 27 17:46 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 646000 Sep 27 17:46 python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2: total 10268 -rw-r--r-- 1 jenkins jenkins 220440 Sep 27 17:51 build.log -rw-r--r-- 1 jenkins jenkins 10136 Sep 27 17:51 consensuscore_1.1.1+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2328 Sep 27 17:51 consensuscore_1.1.1+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 7136 Sep 27 17:51 consensuscore_1.1.1+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8018 Sep 27 17:51 consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2054 Sep 27 17:51 consensuscore_1.1.1+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1371 Sep 27 17:51 consensuscore_1.1.1+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 475924 Sep 27 17:51 libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9124872 Sep 27 17:51 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 646000 Sep 27 17:51 python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb Fri Sep 27 17:51:25 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Fri Sep 27 17:51:26 UTC 2024 I: consensuscore_1.1.1+dfsg-7_arm64.changes: Format: 1.8 Date: Sun, 24 Mar 2024 17:07:25 +0100 Source: consensuscore Binary: libconsensuscore-dev python3-pbconsensuscore python3-pbconsensuscore-dbgsym Architecture: arm64 Version: 1.1.1+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libconsensuscore-dev - algorithms for PacBio multiple sequence consensus -- development python3-pbconsensuscore - algorithms for PacBio multiple sequence consensus -- Python 3 Changes: consensuscore (1.1.1+dfsg-7) unstable; urgency=medium . * Team upload. * d/control: resume building on i386. * d/rules: add openmp-simd and -O3 flags. Checksums-Sha1: 77dc4fb6f186abfcb62808c5bd1f7396a4c5beaf 7136 consensuscore_1.1.1+dfsg-7_arm64.buildinfo 0b9d803edd3573791ba9ad23cdc20dee5a0fedc6 475924 libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb 677c5984445e11db05e990bd8505563c19dc07a4 9124872 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb e32271cc4f662c92cadba3e40e0551280565e9f5 646000 python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb Checksums-Sha256: 6e1f332d847adf88c5e124b05b249ff1badfb5fbefd5c5a3e5249385df239c96 7136 consensuscore_1.1.1+dfsg-7_arm64.buildinfo 70fd9889501bfb4304bbe45dcc383590c80a5a06db163e7aac376869d8026966 475924 libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb 7af8f1538861827b17c06b54369492f8afc11b6b51c5dd740c98d7dbdc38e87c 9124872 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb 91a421c0d3400026e54587a0e0ae6b548b2739a5afdaaa9ba9084dc5a744c30d 646000 python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb Files: 7706d76446cb65d23ecd776f984387cc 7136 science optional consensuscore_1.1.1+dfsg-7_arm64.buildinfo aa1e48ab36e49cab7da694164d52b4a1 475924 libdevel optional libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb 6f61c831cafae08fb041f3c66e7e2ea6 9124872 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb 7fe8d13f9105dc43d5f4446d7e19e009 646000 python optional python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/consensuscore_1.1.1+dfsg-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/consensuscore_1.1.1+dfsg-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/consensuscore_1.1.1+dfsg-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/consensuscore_1.1.1+dfsg-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/consensuscore_1.1.1+dfsg-7_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/consensuscore_1.1.1+dfsg-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-27 17:46:52.359325569 +0000 +++ b2/build.log 2024-09-27 17:51:25.643705906 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Sep 27 05:41:11 -12 2024 -I: pbuilder-time-stamp: 1727458871 +I: Current time: Fri Oct 31 14:09:53 +14 2025 +I: pbuilder-time-stamp: 1761869393 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying portable_simd.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 31 00:10 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='6d5fa6ab37db45d3880e73d9bd8db887' - 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='1096911' - PS1='# ' - PS2='> ' + INVOCATION_ID=7c6352e8ef7a42f9bd0b0babd9211011 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2261779 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.sQlON7a3/pbuilderrc_uOJf --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.sQlON7a3/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/pbuilderrc_mKIh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1096911/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -219,7 +251,7 @@ Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] -Fetched 54.4 MB in 0s (208 MB/s) +Fetched 54.4 MB in 0s (191 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) @@ -512,8 +544,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Sep 27 17:41:49 UTC 2024. -Universal Time is now: Fri Sep 27 17:41:49 UTC 2024. +Local time is now: Fri Oct 31 00:10:16 UTC 2025. +Universal Time is now: Fri Oct 31 00:10:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -590,7 +622,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/consensuscore-1.1.1+dfsg/ && 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 > ../consensuscore_1.1.1+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-7_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -814,8 +850,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, - from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, - from src/C++/Quiver/ReadScorer.cpp:7: + from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, + from src/C++/Quiver/detail/RecursorBase.cpp:6: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ @@ -834,29 +870,15 @@ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simde/x86/sse2.h:35, - from /usr/include/simde/x86/sse3.h:30, - from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Edna/EdnaEvaluator.hpp:6, - from src/C++/Quiver/detail/RecursorBase.cpp:6: -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:468:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 468 | sign_bit = _mm_and_ps(sign_bit, *reinterpret_cast(_ps_sign_mask)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:478:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 478 | emm2 = _mm_add_epi32(emm2, *reinterpret_cast(_pi32_1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:479:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 479 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_inv1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:482:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 482 | emm0 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -882,10 +904,6 @@ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:601:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 601 | emm2 = _mm_and_si128(emm2, *reinterpret_cast(_pi32_2)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: -/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘void sincos_ps(v4sf, v4sf*, v4sf*)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:703:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 703 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); @@ -911,6 +929,24 @@ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simde/x86/sse2.h:35, + from /usr/include/simde/x86/sse3.h:30, + from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/QvEvaluator.hpp:6, + from src/C++/Quiver/ReadScorer.cpp:7: +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf log_ps(v4sf)’: +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:182:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 182 | x, *reinterpret_cast(_ps_min_norm_pos)); /* cut off denormalized stuff */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:193:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 193 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_mant_mask)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:203:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 203 | emm0 = _mm_sub_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf exp_ps(v4sf)’: +/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:347:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 347 | emm0 = _mm_add_epi32(emm0, *reinterpret_cast(_pi32_0x7f)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h: In function ‘v4sf sin_ps(v4sf)’: /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:466:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 466 | x = _mm_and_ps(x, *reinterpret_cast(_ps_inv_sign_mask)); @@ -1061,19 +1097,15 @@ 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/SimpleRecursor.hpp:5, from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/MutationScorer.hpp:12, @@ -1158,6 +1190,7 @@ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here 190 | template class MutationScorer; @@ -1207,6 +1240,9 @@ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o In file included from /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:6, @@ -1297,32 +1333,30 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d In file included from /usr/include/simde/x86/sse2.h:35, from /usr/include/simde/x86/sse3.h:30, from src/C++/Edna/EdnaCounts.cpp:4: @@ -1403,11 +1437,13 @@ /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Quiver/detail/sse_mathfun.h:779:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 779 | emm4 = _mm_andnot_si128(emm4, *reinterpret_cast(_pi32_4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d @@ -1486,37 +1522,37 @@ [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest -[ OK ] RecursorTest/0.SmallMatchTest (0 ms) +[ OK ] RecursorTest/0.SmallMatchTest (1 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest -[ OK ] RecursorTest/0.MediumSizedTest (0 ms) +[ OK ] RecursorTest/0.MediumSizedTest (1 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/0 (1 ms total) +[----------] 7 tests from RecursorTest/0 (2 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest -[ OK ] RecursorTest/1.SmallMatchTest (1 ms) +[ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest -[ OK ] RecursorTest/1.MediumSizedTest (1 ms) +[ OK ] RecursorTest/1.MediumSizedTest (3 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest -[ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) +[ OK ] RecursorTest/1.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/1 (3 ms total) +[----------] 7 tests from RecursorTest/1 (4 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest @@ -1526,14 +1562,14 @@ [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest -[ OK ] RecursorTest/2.MediumSizedTest (2 ms) +[ OK ] RecursorTest/2.MediumSizedTest (4 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest -[ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) +[ OK ] RecursorTest/2.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/2 (2 ms total) +[----------] 7 tests from RecursorTest/2 (5 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest @@ -1543,31 +1579,31 @@ [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest -[ OK ] RecursorTest/3.MediumSizedTest (1 ms) +[ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/3 (8 ms total) +[----------] 7 tests from RecursorTest/3 (4 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (14 ms) +[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (25 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (19 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta -[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (18 ms) +[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (17 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha -[ OK ] RecursorFuzzTest/0.ExtendAlpha (11 ms) +[ OK ] RecursorFuzzTest/0.ExtendAlpha (15 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta -[ OK ] RecursorFuzzTest/0.ExtendBeta (12 ms) -[----------] 5 tests from RecursorFuzzTest/0 (84 ms total) +[ OK ] RecursorFuzzTest/0.ExtendBeta (13 ms) +[----------] 5 tests from RecursorFuzzTest/0 (89 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (25 ms) +[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (27 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (25 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta @@ -1576,61 +1612,61 @@ [ OK ] RecursorFuzzTest/1.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (12 ms) -[----------] 5 tests from RecursorFuzzTest/1 (99 ms total) +[----------] 5 tests from RecursorFuzzTest/1 (101 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (32 ms) [ RUN ] RecursorFuzzTest/2.Alignment -[ OK ] RecursorFuzzTest/2.Alignment (48 ms) +[ OK ] RecursorFuzzTest/2.Alignment (32 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta -[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (73 ms) +[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (36 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha -[ OK ] RecursorFuzzTest/2.ExtendAlpha (19 ms) +[ OK ] RecursorFuzzTest/2.ExtendAlpha (11 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta -[ OK ] RecursorFuzzTest/2.ExtendBeta (19 ms) -[----------] 5 tests from RecursorFuzzTest/2 (203 ms total) +[ OK ] RecursorFuzzTest/2.ExtendBeta (11 ms) +[----------] 5 tests from RecursorFuzzTest/2 (122 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (58 ms) +[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (29 ms) [ RUN ] RecursorFuzzTest/3.Alignment -[ OK ] RecursorFuzzTest/3.Alignment (54 ms) +[ OK ] RecursorFuzzTest/3.Alignment (29 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta -[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (54 ms) +[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (29 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha -[ OK ] RecursorFuzzTest/3.ExtendAlpha (12 ms) +[ OK ] RecursorFuzzTest/3.ExtendAlpha (10 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (11 ms) -[----------] 5 tests from RecursorFuzzTest/3 (203 ms total) +[----------] 5 tests from RecursorFuzzTest/3 (108 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (33 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 -[ OK ] QvEvaluatorTest.DelVsDel4 (34 ms) +[ OK ] QvEvaluatorTest.DelVsDel4 (33 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (39 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (25 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (3 ms) -[----------] 5 tests from QvEvaluatorTest (136 ms total) +[----------] 5 tests from QvEvaluatorTest (133 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest -[ OK ] PoaGraph.SmallBasicTest (1 ms) +[ OK ] PoaGraph.SmallBasicTest (0 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests -[ OK ] PoaGraph.SmallDeletionTests (1 ms) -[----------] 4 tests from PoaGraph (2 ms total) +[ OK ] PoaGraph.SmallDeletionTests (0 ms) +[----------] 4 tests from PoaGraph (0 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple -[ OK ] PoaConsensus.TestSimple (0 ms) +[ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest @@ -1641,13 +1677,13 @@ [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png -sh: 1: dot: not found -[ OK ] PoaConsensus.TestLocalStaggered (26 ms) +sh: line 1: dot: command not found +[ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest -[ OK ] PoaConsensus.NondeterminismRegressionTest (552 ms) -[----------] 8 tests from PoaConsensus (580 ms total) +[ OK ] PoaConsensus.NondeterminismRegressionTest (479 ms) +[----------] 8 tests from PoaConsensus (487 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests @@ -1662,8 +1698,8 @@ [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest -[ OK ] AffineAlignmentTests.LargeGapTest (9 ms) -[----------] 2 tests from AffineAlignmentTests (9 ms total) +[ OK ] AffineAlignmentTests.LargeGapTest (7 ms) +[----------] 2 tests from AffineAlignmentTests (7 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest @@ -1690,11 +1726,11 @@ [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) -[----------] 7 tests from MutationTest (1 ms total) +[----------] 7 tests from MutationTest (0 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest -[ OK ] MutationScorerTest/0.BasicTest (0 ms) +[ OK ] MutationScorerTest/0.BasicTest (1 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning @@ -1725,10 +1761,10 @@ [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest -[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (0 ms) +[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest -[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) -[----------] 8 tests from MutationScorerTest/1 (2 ms total) +[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (0 ms) +[----------] 8 tests from MutationScorerTest/1 (1 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest @@ -1746,8 +1782,8 @@ [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest -[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) -[----------] 8 tests from MutationScorerTest/2 (2 ms total) +[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (0 ms) +[----------] 8 tests from MutationScorerTest/2 (1 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest @@ -1763,7 +1799,7 @@ [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest -[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms) +[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (2 ms total) @@ -1809,9 +1845,9 @@ [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 -[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) +[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (0 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest -[ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) +[ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds @@ -1842,7 +1878,7 @@ [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) -[----------] 11 tests from MatrixTest/0 (2 ms total) +[----------] 11 tests from MatrixTest/0 (1 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic @@ -1863,7 +1899,7 @@ [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 -[ OK ] MatrixTest/1.BigBandedMatrix (5 ms) +[ OK ] MatrixTest/1.BigBandedMatrix (6 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest @@ -1880,7 +1916,7 @@ [----------] 3 tests from CoverageTests (0 ms total) [----------] Global test environment tear-down -[==========] 158 tests from 29 test cases ran. (1354 ms total) +[==========] 158 tests from 29 test cases ran. (1078 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' @@ -1992,8 +2028,8 @@ dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7_arm64.deb'. +dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7_arm64.changes @@ -2002,12 +2038,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2261779/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1096911 and its subdirectories -I: Current time: Fri Sep 27 05:46:51 -12 2024 -I: pbuilder-time-stamp: 1727459211 +I: removing directory /srv/workspace/pbuilder/2261779 and its subdirectories +I: Current time: Fri Oct 31 14:14:22 +14 2025 +I: pbuilder-time-stamp: 1761869662 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/consensuscore_1.1.1+dfsg-7.diff: 90.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/consensuscore_1.1.1+dfsg-7.diff.gz b2/build.log: 91.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 92.2% -- replaced with stdout Fri Sep 27 17:51:27 UTC 2024 I: diffoscope 277 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_consensuscore_unstable_arm64_1727459487 + touch /var/log/reproducible-builds/diffoscope_stamp_consensuscore_unstable_arm64_1727459487 + RESULT=0 + systemd-run '--description=diffoscope on consensuscore/1.1.1+dfsg-7 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_4-37435 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3 --run-session -c jenkins-reproducible-unstable-diffoscope-0a906135-1287-4b9a-ad2c-4be772f02f41 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/dbd-tmp-zaveR2a ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b1/consensuscore_1.1.1+dfsg-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2/consensuscore_1.1.1+dfsg-7_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_4-37435.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/consensuscore_1.1.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b1/consensuscore_1.1.1+dfsg-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sQlON7a3/b2/consensuscore_1.1.1+dfsg-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.514s) 0.514s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.130s) 0.130s 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: 857ms CPU time consumed: 859ms ___ ___ _ __ ___ ___ _ __ ___ _ _ ___ ___ ___ _ __ ___ / __/ _ \| '_ \/ __|/ _ \ '_ \/ __| | | / __|/ __/ _ \| '__/ _ \ | (_| (_) | | | \__ \ __/ | | \__ \ |_| \__ \ (_| (_) | | | __/ \___\___/|_| |_|___/\___|_| |_|___/\__,_|___/\___\___/|_| \___| Fri Sep 27 17:51:28 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 27 17:51:28 UTC 2024 I: consensuscore from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-27 17:51:29] INFO: Starting at 2024-09-27 17:51:29.616045 [2024-09-27 17:51:29] INFO: Generating the pages of 1 package(s) [2024-09-27 17:51:29] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/consensuscore didn't produce a buildlog, even though it has been built. [2024-09-27 17:51:29] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/consensuscore_1.1.1+dfsg-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/consensuscore_1.1.1+dfsg-7.diff.gz is missing [2024-09-27 17:51:30] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/consensuscore_1.1.1+dfsg-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/consensuscore_1.1.1+dfsg-7.diff.gz is missing [2024-09-27 17:51:30] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/consensuscore_1.1.1+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/consensuscore_1.1.1+dfsg-4.diff.gz is missing [2024-09-27 17:51:30] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/consensuscore_1.1.1+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/consensuscore_1.1.1+dfsg-4.diff.gz is missing [2024-09-27 17:51:30] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/consensuscore_1.1.1+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/consensuscore_1.1.1+dfsg-2.diff.gz is missing [2024-09-27 17:51:30] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/consensuscore_1.1.1+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/consensuscore_1.1.1+dfsg-2.diff.gz is missing [2024-09-27 17:51:30] INFO: Finished at 2024-09-27 17:51:30.179869, took: 0:00:00.563829 Fri Sep 27 17:51:30 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/consensuscore.html Fri Sep 27 17:51:30 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Sep 27 17:51:30 UTC 2024 I: Submitting 8.0K b1/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc https://buildinfo.debian.net/77dc4fb6f186abfcb62808c5bd1f7396a4c5beaf/consensuscore_1.1.1+dfsg-7_arm64 Fri Sep 27 17:51:31 UTC 2024 I: Submitting 8.0K b2/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc https://buildinfo.debian.net/3e1bca258a0330919bc0bd9f8b3b221cb31e866b/consensuscore_1.1.1+dfsg-7_arm64 Fri Sep 27 17:51:32 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Sep 27 17:51:32 UTC 2024 I: Done submitting .buildinfo files. Fri Sep 27 17:51:32 UTC 2024 I: Removing signed consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc files: removed './b1/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc' removed './b2/consensuscore_1.1.1+dfsg-7_arm64.buildinfo.asc' 1727459492 arm64 unstable consensuscore Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/consensuscore_1.1.1+dfsg-7.rbuild.log: 91.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/consensuscore_1.1.1+dfsg-7.rbuild.log.gz [2024-09-27 17:51:33] INFO: Starting at 2024-09-27 17:51:33.248688 [2024-09-27 17:51:33] INFO: Generating the pages of 1 package(s) [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/consensuscore_1.1.1+dfsg-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/consensuscore_1.1.1+dfsg-7.diff.gz is missing [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/consensuscore_1.1.1+dfsg-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/consensuscore_1.1.1+dfsg-7.diff.gz is missing [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/consensuscore_1.1.1+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/consensuscore_1.1.1+dfsg-4.diff.gz is missing [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/consensuscore_1.1.1+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/consensuscore_1.1.1+dfsg-4.diff.gz is missing [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/consensuscore_1.1.1+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/consensuscore_1.1.1+dfsg-2.diff.gz is missing [2024-09-27 17:51:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/consensuscore_1.1.1+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/consensuscore_1.1.1+dfsg-2.diff.gz is missing [2024-09-27 17:51:33] INFO: Finished at 2024-09-27 17:51:33.803297, took: 0:00:00.554614 All cleanup done. Fri Sep 27 17:51:33 UTC 2024 - total duration: 0h 10m 22s. Fri Sep 27 17:51:33 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-CrTXH3ni, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 10min 27.940s CPU time consumed: 8.603s