Sun May 12 15:17:37 UTC 2024 I: starting to build rapmap/trixie/arm64 on jenkins on '2024-05-12 15:17' Sun May 12 15:17:37 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_22/10329/console.log Sun May 12 15:17:37 UTC 2024 I: Downloading source for trixie/rapmap=0.15.0+dfsg-4 --2024-05-12 15:17:37-- http://deb.debian.org/debian/pool/main/r/rapmap/rapmap_0.15.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2322 (2.3K) [text/prs.lines.tag] Saving to: ‘rapmap_0.15.0+dfsg-4.dsc’ 0K .. 100% 226M=0s 2024-05-12 15:17:37 (226 MB/s) - ‘rapmap_0.15.0+dfsg-4.dsc’ saved [2322/2322] Sun May 12 15:17:37 UTC 2024 I: rapmap_0.15.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rapmap Binary: rapmap, rapmap-example-data, rapmap-dev Architecture: any all Version: 0.15.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: https://github.com/COMBINE-lab/RapMap Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rapmap Vcs-Git: https://salsa.debian.org/med-team/rapmap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 Package-List: rapmap deb science optional arch=any rapmap-dev deb science optional arch=all rapmap-example-data deb science optional arch=all Checksums-Sha1: 0c4a16003c0d2fe77679260ebdb6e21792f862f0 624916 rapmap_0.15.0+dfsg.orig.tar.xz 32044b4fcb178f5e7b2495f00c5253358ad9d741 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz Checksums-Sha256: 17068c4f664e07bec3ade28d624e5b84ef240b116bcc39e5b495d73b2d87ede5 624916 rapmap_0.15.0+dfsg.orig.tar.xz 4267978d5484cb29f0a7993df95e6ce48006b946cb6e2d8498716db7e40138af 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz Files: c52551692c7480f0c1a46478595dd24b 624916 rapmap_0.15.0+dfsg.orig.tar.xz 624fa352250052cb177e582f3d50161d 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYBufUACgkQPCZ2P2xn 5uL8zRAAgxcnDWblU3dZFeCPt3A1A86+92J2q7BZTAeYdMuybryMTiNeZQyuggo/ Jd4RDWqP8bbGRig6s6wqm9cPNtELDRpjVYMUUgG3ond3b5K2mUJWk9/PaeH6HCne D+JTO0tIzi/IYSAEO3YieqCXTZHpIggqCYB7+bECk1KjV/pjF8PWMRk6NikCuVdM D07xl3IzMsL6/crI+O193JsHtdur/OnSHcnB6mkTbr6HMU/pFZ+RdAWW33RuRj8J O9W9vTQ4O3zZsLwc8kyG7S6OK1p7qM+2lbVln+H/ojvTb6nlPrqxi7+gpfSI+opt VT5ptkJV1rXTLFYTbp12Gd7spSBoZkq0Fv3pJCb0hKYj1gwqj1rgmK4xt4kvU5Sy c4Zu4s5HOGqShskfcp6QCXPmidTFUrYPdHXg2PGGWKu2eHx55DTQlZiWho4NSEMn x0lKGgnOgl/WLgRZuZrZ6mAzRUbJcz6GXmraekWLlhi5UmnFfzsj3sND1ivBbYYz erva/LDvjxPr8SUpclMbYZkw1IHcAsU680o81G3/gHmaW8+kfaKaCrm2cmJQqxRd vXZVixcM6FmKcp8VgIURtL3pedTuQXR1DyZunnmvM2lJyBPXzvN5jIW2y/dH4Gjv JRw1rOujMJDQiynxCclWKNiBXsHN9HTdlCuN5n5Cksp+f6d5uZI= =5gwA -----END PGP SIGNATURE----- Sun May 12 15:17:37 UTC 2024 I: Checking whether the package is not for us Sun May 12 15:17:37 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun May 12 15:17:37 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun May 12 15:18:54 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 03:17:40 -12 2024 I: pbuilder-time-stamp: 1715527060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [rapmap_0.15.0+dfsg-4.dsc] I: copying [./rapmap_0.15.0+dfsg.orig.tar.xz] I: copying [./rapmap_0.15.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 17:52:53 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rapmap_0.15.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting rapmap in rapmap-0.15.0+dfsg dpkg-source: info: unpacking rapmap_0.15.0+dfsg.orig.tar.xz dpkg-source: info: unpacking rapmap_0.15.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-libs.patch dpkg-source: info: applying use_shared_libs.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying spelling dpkg-source: info: applying portable_pause dpkg-source: info: applying no_gomp_needed dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3691683/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='1eb7003db36d4a6595e1a4c23ceb3a05' 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='3691683' 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.fsAnfIAq/pbuilderrc_xq0l --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fsAnfIAq/b1 --logfile b1/build.log rapmap_0.15.0+dfsg-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3691683/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), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19745 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python3-markdown; however: Package python3-markdown is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} catch2{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcereal-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt9{a} libgssapi-krb5-2{a} libicu72{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1.12{a} libssh2-1t64{a} libsub-override-perl{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-importlib-metadata{a} python3-markdown{a} python3-minimal{a} python3-more-itertools{a} python3-typing-extensions{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix python3-pygments python3-yaml wget 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 46.4 MB of archives. After unpacking 197 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 catch2 arm64 3.4.0-1 [551 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.2-2 [321 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 40 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-5 [412 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-1.1 [142 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.29.2-2 [2167 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.29.2-2 [9059 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 62 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libcereal-dev arm64 1.3.2+dfsg-5 [221 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libdivsufsort3 arm64 2.0.1-6 [39.1 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libdivsufsort-dev arm64 2.0.1-6 [18.8 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libfmt9 arm64 9.1.0+ds1-2 [107 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfmt-dev arm64 9.1.0+ds1-2 [171 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-2 arm64 2.3.1-3+b4 [62.0 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-dev arm64 2.3.1-3+b4 [136 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libjemalloc2 arm64 5.3.0-2+b1 [218 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libjemalloc-dev arm64 5.3.0-2+b1 [359 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libspdlog1.12 arm64 1:1.12.0+ds-2+b1 [125 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libspdlog-dev arm64 1:1.12.0+ds-2+b1 [85.5 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 1.0.0-6 [6696 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-markdown all 3.6-1 [84.0 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Fetched 46.4 MB in 0s (137 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19745 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20061 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21053 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. 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Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-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 .../17-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package catch2. Preparing to unpack .../18-catch2_3.4.0-1_arm64.deb ... Unpacking catch2 (3.4.0-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../19-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. 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Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../26-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../27-libkrb5-3_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../28-libgssapi-krb5-2_1.20.1-6+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../29-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../30-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:arm64. 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Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../37-libjsoncpp25_1.9.5-6+b2_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../38-librhash0_1.4.3-3+b1_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../39-libuv1t64_1.48.0-1.1_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-1.1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../40-cmake-data_3.29.2-2_all.deb ... Unpacking cmake-data (3.29.2-2) ... Selecting previously unselected package cmake. Preparing to unpack .../41-cmake_3.29.2-2_arm64.deb ... Unpacking cmake (3.29.2-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../42-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../43-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../44-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../45-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../46-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../47-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../48-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../49-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../50-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../51-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../52-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 .../53-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../54-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package rapidjson-dev. Preparing to unpack .../55-rapidjson-dev_1.1.0+dfsg2-7.2_all.deb ... Unpacking rapidjson-dev (1.1.0+dfsg2-7.2) ... Selecting previously unselected package libcereal-dev. Preparing to unpack .../56-libcereal-dev_1.3.2+dfsg-5_arm64.deb ... Unpacking libcereal-dev (1.3.2+dfsg-5) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../57-libdivsufsort3_2.0.1-6_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-6) ... Selecting previously unselected package libdivsufsort-dev:arm64. Preparing to unpack .../58-libdivsufsort-dev_2.0.1-6_arm64.deb ... Unpacking libdivsufsort-dev:arm64 (2.0.1-6) ... Selecting previously unselected package libfmt9:arm64. Preparing to unpack .../59-libfmt9_9.1.0+ds1-2_arm64.deb ... Unpacking libfmt9:arm64 (9.1.0+ds1-2) ... Selecting previously unselected package libfmt-dev:arm64. Preparing to unpack .../60-libfmt-dev_9.1.0+ds1-2_arm64.deb ... Unpacking libfmt-dev:arm64 (9.1.0+ds1-2) ... Selecting previously unselected package libjellyfish-2.0-2:arm64. Preparing to unpack .../61-libjellyfish-2.0-2_2.3.1-3+b4_arm64.deb ... Unpacking libjellyfish-2.0-2:arm64 (2.3.1-3+b4) ... Selecting previously unselected package libjellyfish-2.0-dev. Preparing to unpack .../62-libjellyfish-2.0-dev_2.3.1-3+b4_arm64.deb ... Unpacking libjellyfish-2.0-dev (2.3.1-3+b4) ... Selecting previously unselected package libjemalloc2:arm64. Preparing to unpack .../63-libjemalloc2_5.3.0-2+b1_arm64.deb ... Unpacking libjemalloc2:arm64 (5.3.0-2+b1) ... Selecting previously unselected package libjemalloc-dev. Preparing to unpack .../64-libjemalloc-dev_5.3.0-2+b1_arm64.deb ... Unpacking libjemalloc-dev (5.3.0-2+b1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../65-libpkgconf3_1.8.1-1+b2_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1+b2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../66-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../67-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package libspdlog1.12:arm64. Preparing to unpack .../68-libspdlog1.12_1%3a1.12.0+ds-2+b1_arm64.deb ... Unpacking libspdlog1.12:arm64 (1:1.12.0+ds-2+b1) ... Selecting previously unselected package libspdlog-dev:arm64. Preparing to unpack .../69-libspdlog-dev_1%3a1.12.0+ds-2+b1_arm64.deb ... Unpacking libspdlog-dev:arm64 (1:1.12.0+ds-2+b1) ... Selecting previously unselected package libtclap-dev. Preparing to unpack .../70-libtclap-dev_1.2.5-1+b1_arm64.deb ... Unpacking libtclap-dev (1.2.5-1+b1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../71-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../72-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../73-pkg-config_1.8.1-1+b2_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-1+b2) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../74-python3-typing-extensions_4.10.0-1_all.deb ... Unpacking python3-typing-extensions (4.10.0-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../75-python3-more-itertools_10.2.0-1_all.deb ... Unpacking python3-more-itertools (10.2.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../76-python3-zipp_1.0.0-6_all.deb ... Unpacking python3-zipp (1.0.0-6) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../77-python3-importlib-metadata_4.12.0-1_all.deb ... Unpacking python3-importlib-metadata (4.12.0-1) ... 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Setting up libjsoncpp25:arm64 (1.9.5-6+b2) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtclap-dev (1.2.5-1+b1) ... Setting up libfmt9:arm64 (9.1.0+ds1-2) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up librhash0:arm64 (1.4.3-3+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up cmake-data (3.29.2-2) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libdivsufsort3:arm64 (2.0.1-6) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libdivsufsort-dev:arm64 (2.0.1-6) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rapmap-0.15.0+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 > ../rapmap_0.15.0+dfsg-4_source.changes dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.15.0+dfsg-4 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 debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true .. CC: gcc CC version: -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.6.0 -- DISABLING NATIVE ARCH. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Making Default build type -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3") -- Found Cereal: /usr/include (Required is at least version "1.2.2") -- Cereal found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/aarch64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = .git/ CMAKE_SYSTEM_PROCESSOR: aarch64 -- Configuring done (2.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED JELLYFISH_ROOT -- Build files have been written to: /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rapmap-0.15.0+dfsg -B/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/depend make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg.c [ 30%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration 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-MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2_sse.c [ 38%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 38%] Built target ksw2pp_sse2 make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 38%] Built target ksw2pp_basic make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 42%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o 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-fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp [ 76%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o [ 76%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -MF CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapFileSystem.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp [ 80%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o [ 84%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o cd 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-Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -MF CMakeFiles/rapmap.dir/FastxParser.cpp.o.d -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/rank9b.cpp.o -MF CMakeFiles/rapmap.dir/rank9b.cpp.o.d -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/rank9b.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/stringpiece.cc.o -MF CMakeFiles/rapmap.dir/stringpiece.cc.o.d -o CMakeFiles/rapmap.dir/stringpiece.cc.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/stringpiece.cc cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/xxhash.c.o -MF CMakeFiles/rapmap.dir/xxhash.c.o.d -o CMakeFiles/rapmap.dir/xxhash.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/xxhash.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/bit_array.c.o -MF CMakeFiles/rapmap.dir/bit_array.c.o.d -o CMakeFiles/rapmap.dir/bit_array.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/bit_array.c [ 92%] Building CXX object src/CMakeFiles/rapmap.dir/edlib.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/edlib.cpp.o -MF CMakeFiles/rapmap.dir/edlib.cpp.o.d -o CMakeFiles/rapmap.dir/edlib.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/edlib.cpp [ 96%] Building CXX object src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -MF CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/FastxParser.hpp:17, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp:1: /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3228:26: required from 'void moodycamel::ConcurrentQueue::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue::ImplicitProducerKVP&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3221:4: required from 'moodycamel::ConcurrentQueue::ImplicitProducerKVP& moodycamel::ConcurrentQueue::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue::ImplicitProducerKVP&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' /usr/include/c++/13/bits/move.h:198:11: required from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]' /usr/include/c++/13/bits/stl_algobase.h:185:11: required from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' /usr/include/c++/13/bits/stl_algobase.h:215:16: required from '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' /usr/include/c++/13/array:121:25: required from 'void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue, std::default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]' /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3264:42: required from 'void moodycamel::ConcurrentQueue::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:892:3: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::swap_internal(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:863:10: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::operator=(moodycamel::ConcurrentQueue&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp:46:14: required from 'fastx_parser::FastxParser::FastxParser(std::vector >, std::vector >, uint32_t, uint32_t, uint32_t) [with T = fastx_parser::ReadSeq; uint32_t = unsigned int]' /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp:405:16: required from here /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:446:19: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 446 | T temp = std::move(left.load(std::memory_order_relaxed)); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:446:19: note: remove 'std::move' call /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:447:27: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 447 | left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/concurrentqueue.h:447:27: note: remove 'std::move' call In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/zstr.hpp:16, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:62: /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const std::string&, std::ios_base::openmode)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 128 | catch (std::ios_base::failure e) {} | ^ cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:73: In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from 'void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from 'digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]' at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:581:30: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:5: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics [100%] Linking CXX executable rapmap cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/rapmap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wl,-z,relro -Wl,-z,now CMakeFiles/rapmap.dir/RapMap.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o CMakeFiles/rapmap.dir/HitManager.cpp.o CMakeFiles/rapmap.dir/FastxParser.cpp.o CMakeFiles/rapmap.dir/rank9b.cpp.o CMakeFiles/rapmap.dir/stringpiece.cc.o CMakeFiles/rapmap.dir/xxhash.c.o CMakeFiles/rapmap.dir/bit_array.c.o CMakeFiles/rapmap.dir/edlib.cpp.o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -o rapmap -L/build/reproducible-path/rapmap-0.15.0+dfsg/lib -L/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" /usr/lib/aarch64-linux-gnu/libz.so -ldivsufsort -ldivsufsort64 -lm -lz /usr/lib/aarch64-linux-gnu/libjemalloc.so -lrt libksw2pp.a -ldl /usr/bin/ld: libksw2pp.a(KSW2Aligner.cpp.o): in function `ksw2pp::KSW2Aligner::operator()(unsigned char const*, int, unsigned char const*, int, ksw_extz_t*, ksw2pp::EnumToType<(ksw2pp::KSW2AlignmentType)2>)': ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:362:(.text+0x284): undefined reference to `ksw_extz2_sse2' /usr/bin/ld: ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:358:(.text+0x2b8): undefined reference to `ksw_extz2_sse41' /usr/bin/ld: libksw2pp.a(KSW2Aligner.cpp.o): in function `ksw2pp::KSW2Aligner::operator()(char const*, int, char const*, int, ksw_extz_t*, ksw2pp::EnumToType<(ksw2pp::KSW2AlignmentType)2>)': ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:227:(.text+0x1084): undefined reference to `ksw_extz2_sse2' /usr/bin/ld: ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:223:(.text+0x10e0): undefined reference to `ksw_extz2_sse41' collect2: error: ld returned 1 exit status make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:311: src/rapmap] Error 1 make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:134: src/CMakeFiles/rapmap.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' make: *** [debian/rules:17: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3691683 and its subdirectories Sun May 12 15:18:56 UTC 2024 W: No second build log, what happened?