Mon Apr 29 14:23:50 UTC 2024 I: starting to build idba/trixie/arm64 on jenkins on '2024-04-29 14:23' Mon Apr 29 14:23:50 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/16306/console.log Mon Apr 29 14:23:50 UTC 2024 I: Downloading source for trixie/idba=1.1.3-8 --2024-04-29 14:23:51-- http://deb.debian.org/debian/pool/main/i/idba/idba_1.1.3-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2022 (2.0K) [text/prs.lines.tag] Saving to: ‘idba_1.1.3-8.dsc’ 0K . 100% 306M=0s 2024-04-29 14:23:51 (306 MB/s) - ‘idba_1.1.3-8.dsc’ saved [2022/2022] Mon Apr 29 14:23:51 UTC 2024 I: idba_1.1.3-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: idba Binary: idba, idba-extra Architecture: any Version: 1.1.3-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/loneknightpy/idba Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/idba Vcs-Git: https://salsa.debian.org/med-team/idba.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libgtest-dev , python3 Package-List: idba deb science optional arch=any idba-extra deb science optional arch=any Checksums-Sha1: cf673154a9696215648177f0bc43b9cc25feaf26 446227 idba_1.1.3.orig.tar.gz 895352f0b6cbf98d8f9fa02df13f9c80807f2fbe 263136 idba_1.1.3-8.debian.tar.xz Checksums-Sha256: 030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0 446227 idba_1.1.3.orig.tar.gz 89c37bdd6d8b98b75c81ff5347bf12b53fdc31b97cbb06021aa742636873daef 263136 idba_1.1.3-8.debian.tar.xz Files: 41fe7eabdcfaea677558f3e4baeb2ea8 446227 idba_1.1.3.orig.tar.gz 69a68d8d6501e6ff89cfafeab18e7273 263136 idba_1.1.3-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNmx/wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEXzBAAiUIMXUls6FrY7PCQyJh0eeys94UaasPX nl8/9hIx3YQG1VeOd8mevfhF9My5acvFeugBB04UBY2DzwZVlJW2a4Vjq2pGuwWv aRE3PtllhXBYnitNP9DuRkL5D5Qz6S28M6UeAMaMveKYW4jPF7N3kDEd4WgN2n8R 7BGl9SExZHScMPo7XS8fyQPKbybBTpg4y//7M+Z86kkHfNRUXVlAMBaRYW18GAir 86PYAGFz/JxgjqEHP6WQTttAraq0tdVE1tB5uX9oi49J49nnFZMR3BDivzZXRuEb qwVvyQxvWgUKTMm2hwqOlCETtZLhN5Ic9KcXlAzjTNe1zVwsW97n6REDStusBGWm o2+z4Lj61qeDpdn1zWQiGlHPDEsm3ayWu0UgfwSEBYDVZxCVzK1bC1icLgMsRU8P e4+Y0r/bi7bvtzckYVdd/8q+9Ksirlihmc/YVyb3Hv55hdnexzrc8wHr5I+7PL3p YGAblq68cpjrb6kbghFj61QxtRgnUeUpPs1bomwM+Q0mjh+wREyPZ45cAVcCwXWv r6Z5uydp4VEmQWe+DQet3XruN4t39Fh3EvKELD4I24EPMEzk66l0zD/5PSl1+Osr ZpM/7Wp4lw2g69kErKjxiUBOYnjyLGiPQWBqePdoWz/LDC0YxyJnwgcFerWj+KsT j4H+3ptYUfQ= =O32F -----END PGP SIGNATURE----- Mon Apr 29 14:23:51 UTC 2024 I: Checking whether the package is not for us Mon Apr 29 14:23:51 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Mon Apr 29 14:23:51 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Mon Apr 29 14:27:06 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 29 02:23:54 -12 2024 I: pbuilder-time-stamp: 1714400634 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 [idba_1.1.3-8.dsc] I: copying [./idba_1.1.3.orig.tar.gz] I: copying [./idba_1.1.3-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 5 20:30:52 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./idba_1.1.3-8.dsc: no acceptable signature found dpkg-source: info: extracting idba in idba-1.1.3 dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz dpkg-source: info: unpacking idba_1.1.3-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install_all_idba_flavours.patch dpkg-source: info: applying use-atomic-for-mips.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_packaged_googletest.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2353803/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='d02c143178c4446b8e252fd97c331d27' 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='2353803' 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.I5Grg31z/pbuilderrc_FLXF --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.I5Grg31z/b1 --logfile b1/build.log idba_1.1.3-8.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 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2353803/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), libgtest-dev, 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 ... 19941 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 libgtest-dev; however: Package libgtest-dev 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 81.0 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: python3 but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 4) libexpat1 [2.6.2-1 (testing)] 5) libpython3-stdlib [3.11.8-1 (testing)] 6) libpython3.11-minimal [3.11.9-1 (testing)] 7) libpython3.11-stdlib [3.11.9-1 (testing)] 8) libreadline8t64 [8.2-4 (testing)] 9) libssl3t64 [3.2.1-3 (testing)] 10) media-types [10.1.0 (testing)] 11) netbase [6.4 (testing)] 12) python3 [3.11.8-1 (testing)] 13) python3-minimal [3.11.8-1 (testing)] 14) python3.11 [3.11.9-1 (testing)] 15) python3.11-minimal [3.11.9-1 (testing)] 16) readline-common [8.2-4 (testing)] 17) tzdata [2024a-3 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdb5.3t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 47 newly installed, 2 to remove and 0 not upgraded. Need to get 28.2 MB of archives. After unpacking 108 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [625 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 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 1:5.45-2+b1 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 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 1.23.0-3+b1 [1126 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 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 2.12.0-3 [1385 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 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 googletest all 1.14.0-1 [512 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libgtest-dev arm64 1.14.0-1+b1 [241 kB] Fetched 28.2 MB in 0s (131 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. libpam-modules:arm64 depends on libdb5.3. (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 ... 19941 files and directories currently installed.) Removing libdb5.3:arm64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64: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 ... 19934 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_arm64.deb ... Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19940 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64: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 ... 19927 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... 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 ... 19942 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 ... 20258 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-3_all.deb ... Unpacking tzdata (2024a-3) ... 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) ... 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Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgtest-dev:arm64 (1.14.0-1+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Processing triggers for libc-bin (2.37-18) ... 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/idba-1.1.3/ && 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 > ../idba_1.1.3-8_source.changes dpkg-buildpackage: info: source package idba dpkg-buildpackage: info: source version 1.1.3-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:429: AM_INIT_AUTOMAKE is expanded from... configure.ac:8: the top level configure.ac:30: warning: AC_OUTPUT should be used without arguments. configure.ac:30: You should run autoupdate. configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation bin/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') bin/Makefile.am:9: warning: source file '$(top_srcdir)/src/tools/fa2fq.cpp' is in a subdirectory, bin/Makefile.am:9: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. bin/Makefile.am:19: warning: source file '$(top_srcdir)/src/tools/filter_blat.cpp' is in a subdirectory, bin/Makefile.am:19: but option 'subdir-objects' is disabled bin/Makefile.am:17: warning: source file '$(top_srcdir)/src/tools/filter_contigs.cpp' is in a subdirectory, bin/Makefile.am:17: but option 'subdir-objects' is disabled bin/Makefile.am:33: warning: source file '$(top_srcdir)/src/release/filterfa.cpp' is in a subdirectory, bin/Makefile.am:33: but option 'subdir-objects' is disabled bin/Makefile.am:25: warning: source file '$(top_srcdir)/src/release/fq2fa.cpp' is in a subdirectory, bin/Makefile.am:25: but option 'subdir-objects' is disabled bin/Makefile.am:34: warning: source file '$(top_srcdir)/src/release/idba.cpp' is in a subdirectory, bin/Makefile.am:34: but option 'subdir-objects' is disabled bin/Makefile.am:30: warning: source file '$(top_srcdir)/src/release/idba_hybrid.cpp' is in a subdirectory, bin/Makefile.am:30: but option 'subdir-objects' is disabled bin/Makefile.am:29: warning: source file '$(top_srcdir)/src/release/idba_tran.cpp' is in a subdirectory, bin/Makefile.am:29: but option 'subdir-objects' is disabled bin/Makefile.am:13: warning: source file '$(top_srcdir)/src/tools/idba_tran_test.cpp' is in a subdirectory, bin/Makefile.am:13: but option 'subdir-objects' is disabled bin/Makefile.am:27: warning: source file '$(top_srcdir)/src/release/idba_ud.cpp' is in a subdirectory, bin/Makefile.am:27: but option 'subdir-objects' is disabled bin/Makefile.am:31: warning: source file '$(top_srcdir)/src/release/parallel_blat.cpp' is in a subdirectory, bin/Makefile.am:31: but option 'subdir-objects' is disabled bin/Makefile.am:18: warning: source file '$(top_srcdir)/src/tools/parallel_rna_blat.cpp' is in a subdirectory, bin/Makefile.am:18: but option 'subdir-objects' is disabled bin/Makefile.am:12: warning: source file '$(top_srcdir)/src/tools/print_graph.cpp' is in a subdirectory, bin/Makefile.am:12: but option 'subdir-objects' is disabled bin/Makefile.am:28: warning: source file '$(top_srcdir)/src/release/raw_n50.cpp' is in a subdirectory, bin/Makefile.am:28: but option 'subdir-objects' is disabled bin/Makefile.am:14: warning: source file '$(top_srcdir)/src/tools/sample_reads.cpp' is in a subdirectory, bin/Makefile.am:14: but option 'subdir-objects' is disabled bin/Makefile.am:7: warning: source file '$(top_srcdir)/src/tools/scaffold.cpp' is in a subdirectory, bin/Makefile.am:7: but option 'subdir-objects' is disabled bin/Makefile.am:6: warning: source file '$(top_srcdir)/src/tools/shuffle_reads.cpp' is in a subdirectory, bin/Makefile.am:6: but option 'subdir-objects' is disabled bin/Makefile.am:36: warning: source file '$(top_srcdir)/src/release/sim_reads.cpp' is in a subdirectory, bin/Makefile.am:36: but option 'subdir-objects' is disabled bin/Makefile.am:32: warning: source file '$(top_srcdir)/src/release/sim_reads_tran.cpp' is in a subdirectory, bin/Makefile.am:32: but option 'subdir-objects' is disabled bin/Makefile.am:15: warning: source file '$(top_srcdir)/src/tools/sort_psl.cpp' is in a subdirectory, bin/Makefile.am:15: but option 'subdir-objects' is disabled bin/Makefile.am:16: warning: source file '$(top_srcdir)/src/tools/sort_reads.cpp' is in a subdirectory, bin/Makefile.am:16: but option 'subdir-objects' is disabled bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory, bin/Makefile.am:20: but option 'subdir-objects' is disabled bin/Makefile.am:23: warning: source file '$(top_srcdir)/src/tools/split_fq.cpp' is in a subdirectory, bin/Makefile.am:23: but option 'subdir-objects' is disabled bin/Makefile.am:35: warning: source file '$(top_srcdir)/src/release/split_scaffold.cpp' is in a subdirectory, bin/Makefile.am:35: but option 'subdir-objects' is disabled bin/Makefile.am:21: warning: source file '$(top_srcdir)/src/tools/test.cpp' is in a subdirectory, bin/Makefile.am:21: but option 'subdir-objects' is disabled bin/Makefile.am:8: warning: source file '$(top_srcdir)/src/tools/validate_component.cpp' is in a subdirectory, bin/Makefile.am:8: but option 'subdir-objects' is disabled bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory, bin/Makefile.am:26: but option 'subdir-objects' is disabled bin/Makefile.am:11: warning: source file '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' is in a subdirectory, bin/Makefile.am:11: but option 'subdir-objects' is disabled bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory, bin/Makefile.am:22: but option 'subdir-objects' is disabled bin/Makefile.am:10: warning: source file '$(top_srcdir)/src/tools/validate_rna.cpp' is in a subdirectory, bin/Makefile.am:10: but option 'subdir-objects' is disabled lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/hash_aligner.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/options_description.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/blat_record.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_reader.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/compact_sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph_branch_group.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/scaffold_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph_branch_group.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_info.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/local_assembler.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/assembly_utility.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, lib/Makefile.am:68: but option 'subdir-objects' is disabled lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest-all.cc' is in a subdirectory, lib/Makefile.am:68: but option 'subdir-objects' is disabled test/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') test/Makefile.am:11: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:11: but option 'subdir-objects' is disabled test/Makefile.am:11: warning: source file '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' is in a subdirectory, test/Makefile.am:11: but option 'subdir-objects' is disabled test/Makefile.am:8: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:8: but option 'subdir-objects' is disabled test/Makefile.am:8: warning: source file '$(top_srcdir)/src/test/bit_edges_unittest.cpp' is in a subdirectory, test/Makefile.am:8: but option 'subdir-objects' is disabled test/Makefile.am:6: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:6: but option 'subdir-objects' is disabled test/Makefile.am:6: warning: source file '$(top_srcdir)/src/test/compact_sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:6: but option 'subdir-objects' is disabled test/Makefile.am:17: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:17: but option 'subdir-objects' is disabled test/Makefile.am:17: warning: source file '$(top_srcdir)/src/test/hash_map_unittest.cpp' is in a subdirectory, test/Makefile.am:17: but option 'subdir-objects' is disabled test/Makefile.am:10: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:10: but option 'subdir-objects' is disabled test/Makefile.am:10: warning: source file '$(top_srcdir)/src/test/hash_set_unittest.cpp' is in a subdirectory, test/Makefile.am:10: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/test/hash_table_unittest.cpp' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:13: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:13: but option 'subdir-objects' is disabled test/Makefile.am:13: warning: source file '$(top_srcdir)/src/test/histgram_unittest.cpp' is in a subdirectory, test/Makefile.am:13: but option 'subdir-objects' is disabled test/Makefile.am:9: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:9: but option 'subdir-objects' is disabled test/Makefile.am:9: warning: source file '$(top_srcdir)/src/test/kmer_unittest.cpp' is in a subdirectory, test/Makefile.am:9: but option 'subdir-objects' is disabled test/Makefile.am:14: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:14: but option 'subdir-objects' is disabled test/Makefile.am:14: warning: source file '$(top_srcdir)/src/test/managed_list_unittest.cpp' is in a subdirectory, test/Makefile.am:14: but option 'subdir-objects' is disabled test/Makefile.am:15: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:15: but option 'subdir-objects' is disabled test/Makefile.am:15: warning: source file '$(top_srcdir)/src/test/sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:15: but option 'subdir-objects' is disabled test/Makefile.am:16: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:16: but option 'subdir-objects' is disabled test/Makefile.am:16: warning: source file '$(top_srcdir)/src/test/short_sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:16: but option 'subdir-objects' is disabled test/Makefile.am:12: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:12: but option 'subdir-objects' is disabled test/Makefile.am:12: warning: source file '$(top_srcdir)/src/test/vertex_status_unittest.cpp' is in a subdirectory, test/Makefile.am:12: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" LIBS=" -latomic" ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" "LIBS= -latomic" checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for working memcmp... yes checking for vprintf... yes checking for sqrt... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating lib/Makefile config.status: creating test/Makefile config.status: creating script/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' make all-recursive make[2]: Entering directory '/build/reproducible-path/idba-1.1.3' Making all in lib make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/lib' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp ../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()': ../src/misc/log.cpp:78:13: warning: 'throw' will always call 'terminate' [-Wterminate] 78 | throw runtime_error("cannot kill log process"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/misc/log.cpp:78:13: note: in C++11 destructors default to 'noexcept' In file included from ../src/container/hash_map.h:14, from ../src/misc/hash_aligner.h:14, from ../src/misc/hash_aligner.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/functional:49, from ../src/basic/functional.h:13, from ../src/container/hash_map.h:13: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)': ../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 122 | write(log_thread.out_fd, line, len); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/graph/contig_graph_branch_group.h:15, from ../src/graph/contig_graph_branch_group.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../src/graph/contig_graph_branch_group.h:13: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/graph/contig_graph.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/graph/contig_graph.h:14: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/graph/hash_graph_branch_group.h:14, from ../src/graph/hash_graph_branch_group.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/graph/hash_graph.h:15: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/graph/scaffold_graph.h:19, from ../src/graph/scaffold_graph.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../src/graph/scaffold_graph.h:14: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/graph/hash_graph.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/graph/hash_graph.h:15: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/assembly/assembly_utility.cpp:14: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/assembly/assembly_utility.h:17, from ../src/assembly/assembly_utility.cpp:9: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque&, std::deque&)': ../src/graph/contig_graph.cpp:1391:30: warning: variable 'end' set but not used [-Wunused-but-set-variable] 1391 | ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component); | ^~~ In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/assembly/local_assembler.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/assembly/assembly_utility.h:17, from ../src/assembly/local_assembler.h:13: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)': ../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable] 488 | bool flag = false; | ^~~~ ../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable] 489 | int aligned[2] = {0}; | ^~~~~~~ In file included from ../gtest_src/gtest/gtest-all.cc:39: ../gtest_src/gtest/gtest.h: In static member function 'static const char* testing::internal::String::CloneCString(const char*)': ../gtest_src/gtest/gtest.h:2672:17: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2672 | return strncpy(dest, src, n); | ^ ../gtest_src/gtest/gtest-all.cc:2155:39: note: length computed here 2155 | NULL : CloneString(c_str, strlen(c_str)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f libassembly.a ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a rm -f libgtest.a ar cru libgtest.a gtest_main.o gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/lib' Making all in bin make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/bin' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/tools/print_graph.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/graph/contig_graph.h:14: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/release/idba_ud.cpp:21: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/release/idba_ud.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/tools/validate_component.cpp: In function 'int main(int, char**)': ../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable] 141 | int ref_id = dict[record.ref_name]; | ^~~~~~ In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/release/idba.cpp:23: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/release/idba.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/tools/scaffold.cpp:21: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ ../src/tools/validate_rna.cpp: In function 'int main(int, char**)': ../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 396 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/tools/scaffold.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/release/idba_tran.cpp:22: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/release/idba_tran.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/release/idba_hybrid.cpp:21: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/release/idba_hybrid.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)': ../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 218 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 219 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 220 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 222 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, from ../src/tools/idba_tran_test.cpp:21: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/tools/idba_tran_test.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque&, ContigGraph&, std::deque&)': ../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 241 | if (flag && path.size() > option.min_transcript) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)': ../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 523 | if (transcripts[i].size() >= option.min_transcript) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp ../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive 6 | #include "graph/contig_graph.h"; | ^ ../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive 7 | #include "sequence/sequence.h"; | ^ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp ../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const std::string&)': ../src/tools/parallel_rna_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 47 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const std::string&)': ../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function 'void Append(const std::string&, const std::string&)': ../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const std::string&)': ../src/tools/parallel_rna_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/tools/test.cpp:6: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../src/tools/test.cpp:1: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp ../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)': ../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp ../src/release/parallel_blat.cpp: In function 'void CreateFile(const std::string&)': ../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 47 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function 'void RemoveFile(const std::string&)': ../src/release/parallel_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function 'void Append(const std::string&, const std::string&)': ../src/release/parallel_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function 'void RunBlat(const std::string&)': ../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)': ../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | fscanf(flist, "%s %lf", buf, &weight[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' Making all in test make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' Making all in script make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' # /usr/bin/make unittest export PATH=/build/reproducible-path/idba-1.1.3/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games && cd test && /usr/bin/make check make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/test' /usr/bin/make compact_sequence_unittest hash_table_unittest bit_edges_unittest kmer_unittest hash_set_unittest atomic_integer_unittest vertex_status_unittest histgram_unittest managed_list_unittest sequence_unittest short_sequence_unittest hash_map_unittest make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o compact_sequence_unittest.o `test -f '../src/test/compact_sequence_unittest.cpp' || echo './'`../src/test/compact_sequence_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o compact_sequence_unittest gtest_main.o compact_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_table_unittest.o `test -f '../src/test/hash_table_unittest.cpp' || echo './'`../src/test/hash_table_unittest.cpp In file included from ../src/container/hash_table.h:23, from ../src/test/hash_table_unittest.cpp:11: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /usr/include/gtest/gtest.h:54, from ../src/test/hash_table_unittest.cpp:9: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_table_unittest gtest_main.o hash_table_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bit_edges_unittest.o `test -f '../src/test/bit_edges_unittest.cpp' || echo './'`../src/test/bit_edges_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o bit_edges_unittest gtest_main.o bit_edges_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o kmer_unittest.o `test -f '../src/test/kmer_unittest.cpp' || echo './'`../src/test/kmer_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o kmer_unittest gtest_main.o kmer_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_set_unittest.o `test -f '../src/test/hash_set_unittest.cpp' || echo './'`../src/test/hash_set_unittest.cpp In file included from ../src/container/hash_set.h:13, from ../src/test/hash_set_unittest.cpp:12: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /usr/include/gtest/gtest.h:54, from ../src/test/hash_set_unittest.cpp:10: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_set_unittest gtest_main.o hash_set_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o atomic_integer_unittest.o `test -f '../src/test/atomic_integer_unittest.cpp' || echo './'`../src/test/atomic_integer_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o atomic_integer_unittest gtest_main.o atomic_integer_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vertex_status_unittest.o `test -f '../src/test/vertex_status_unittest.cpp' || echo './'`../src/test/vertex_status_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vertex_status_unittest gtest_main.o vertex_status_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o histgram_unittest.o `test -f '../src/test/histgram_unittest.cpp' || echo './'`../src/test/histgram_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o histgram_unittest gtest_main.o histgram_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o managed_list_unittest.o `test -f '../src/test/managed_list_unittest.cpp' || echo './'`../src/test/managed_list_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o managed_list_unittest gtest_main.o managed_list_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sequence_unittest.o `test -f '../src/test/sequence_unittest.cpp' || echo './'`../src/test/sequence_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequence_unittest gtest_main.o sequence_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o short_sequence_unittest.o `test -f '../src/test/short_sequence_unittest.cpp' || echo './'`../src/test/short_sequence_unittest.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o short_sequence_unittest gtest_main.o short_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hash_map_unittest.o `test -f '../src/test/hash_map_unittest.cpp' || echo './'`../src/test/hash_map_unittest.cpp In file included from ../src/container/hash_map.h:14, from ../src/test/hash_map_unittest.cpp:11: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /usr/include/gtest/gtest.h:54, from ../src/test/hash_map_unittest.cpp:9: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_map_unittest gtest_main.o hash_map_unittest.o ../lib/libassembly.a -lgtest -latomic make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' /usr/bin/make check-TESTS make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' make[4]: Entering directory '/build/reproducible-path/idba-1.1.3/test' PASS: compact_sequence_unittest PASS: hash_table_unittest PASS: bit_edges_unittest PASS: kmer_unittest PASS: hash_set_unittest PASS: atomic_integer_unittest PASS: vertex_status_unittest PASS: histgram_unittest PASS: managed_list_unittest PASS: sequence_unittest PASS: short_sequence_unittest PASS: hash_map_unittest ============================================================================ Testsuite summary for idba 1.1.3 ============================================================================ # TOTAL: 12 # PASS: 12 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/idba-1.1.3/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' Making install in lib make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/lib' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/lib' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/lib' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/lib' Making install in bin make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/bin' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/bin' /usr/bin/mkdir -p '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' Making install in test make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/test' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/test' Making install in script make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' /usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' make[2]: Entering directory '/build/reproducible-path/idba-1.1.3' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' dh_install # for the moment the role of these scripts is totally unknown but they do not seem to be necessary mv debian/idba/usr/bin/*.py debian/idba/usr/lib/idba/ mv debian/idba/usr/bin/validate_blat* debian/idba/usr/lib/idba/ make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'idba' in '../idba_1.1.3-8_arm64.deb'. dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_arm64.deb'. dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_arm64.deb'. dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../idba_1.1.3-8_arm64.buildinfo dpkg-genchanges --build=binary -O../idba_1.1.3-8_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/2353803 and its subdirectories I: Current time: Mon Apr 29 02:26:58 -12 2024 I: pbuilder-time-stamp: 1714400818 Mon Apr 29 14:27:07 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Apr 29 14:27:07 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Apr 29 14:30:11 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Apr 29 14:30:12 UTC 2024 I: idba_1.1.3-8_arm64.changes: Format: 1.8 Date: Sat, 05 Nov 2022 21:27:52 +0100 Source: idba Binary: idba idba-dbgsym idba-extra idba-extra-dbgsym Architecture: arm64 Version: 1.1.3-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: idba - iterative De Bruijn Graph short read assemblers idba-extra - iterative De Bruijn Graph short read assemblers (extra tools) Changes: idba (1.1.3-8) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Fix dh_missingwq Checksums-Sha1: 302015966a3d19d799885b52c31334c271658b42 13150344 idba-dbgsym_1.1.3-8_arm64.deb 21ff0b758e601013281226570b317204aa4f6363 9329540 idba-extra-dbgsym_1.1.3-8_arm64.deb 931c0a72bc142455f6cf4eed4d53638de505efb4 349916 idba-extra_1.1.3-8_arm64.deb f5c774cc8cea013d753d6f7908730650da49c8a6 6142 idba_1.1.3-8_arm64.buildinfo d034a145017034e2e4829ae7d63ccceeace33741 607308 idba_1.1.3-8_arm64.deb Checksums-Sha256: 273cb000e9d55ba4581111abda53b013b0ebd107c59778fa069d9ffc59765484 13150344 idba-dbgsym_1.1.3-8_arm64.deb f3c29e29b5d230ba1adac3268f387cfb0afabd82c010fecdeea16f76f97de888 9329540 idba-extra-dbgsym_1.1.3-8_arm64.deb 1ab398127d0d1bc0c5bd44d2450cbc685e3f8fa3308a03b501812602cb20bb4c 349916 idba-extra_1.1.3-8_arm64.deb 400e2ead053fc4ec83f669ac174659b908dfe6885f22be30280224f5060af749 6142 idba_1.1.3-8_arm64.buildinfo 3ed6716c28806ef332f49af9f1e229a8ab537f25fa595aff57fbb3ae7817365b 607308 idba_1.1.3-8_arm64.deb Files: 60f6ba5e10ac6d868d2ac84ab96885f8 13150344 debug optional idba-dbgsym_1.1.3-8_arm64.deb 935115a088b17c4cb167cd57ce01380e 9329540 debug optional idba-extra-dbgsym_1.1.3-8_arm64.deb 71f0fc267a29f42059e99710b06af18f 349916 science optional idba-extra_1.1.3-8_arm64.deb 62eb1867ef959e4b834f384e4faeee7c 6142 science optional idba_1.1.3-8_arm64.buildinfo 0c93f026694337daac25dbedfe9a282b 607308 science optional idba_1.1.3-8_arm64.deb Mon Apr 29 14:30:14 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_20-16306.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.I5Grg31z/idba_1.1.3-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.I5Grg31z/idba_1.1.3-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.I5Grg31z/idba_1.1.3-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.I5Grg31z/b1/idba_1.1.3-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.I5Grg31z/b2/idba_1.1.3-8_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: 0.582s) 0.582s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.264s) 0.264s 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: 890ms CPU time consumed: 886ms Mon Apr 29 14:30:15 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 29 14:30:15 UTC 2024 I: idba from trixie built successfully and reproducibly on arm64. Mon Apr 29 14:30:17 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Apr 29 14:30:17 UTC 2024 I: Submitting 8.0K b1/idba_1.1.3-8_arm64.buildinfo.asc Mon Apr 29 14:30:21 UTC 2024 I: Submitting 8.0K b2/idba_1.1.3-8_arm64.buildinfo.asc Mon Apr 29 14:30:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 29 14:30:24 UTC 2024 I: Done submitting .buildinfo files. Mon Apr 29 14:30:24 UTC 2024 I: Removing signed idba_1.1.3-8_arm64.buildinfo.asc files: removed './b1/idba_1.1.3-8_arm64.buildinfo.asc' removed './b2/idba_1.1.3-8_arm64.buildinfo.asc'