Thu May 16 18:56:44 UTC 2024 I: starting to build ivar/trixie/armhf on jenkins on '2024-05-16 18:56' Thu May 16 18:56:44 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_4/5490/console.log Thu May 16 18:56:44 UTC 2024 I: Downloading source for trixie/ivar=1.4.2+dfsg-3 --2024-05-16 18:56:44-- http://deb.debian.org/debian/pool/main/i/ivar/ivar_1.4.2%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2205 (2.2K) [text/prs.lines.tag] Saving to: ‘ivar_1.4.2+dfsg-3.dsc’ 0K .. 100% 172M=0s 2024-05-16 18:56:44 (172 MB/s) - ‘ivar_1.4.2+dfsg-3.dsc’ saved [2205/2205] Thu May 16 18:56:44 UTC 2024 I: ivar_1.4.2+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.4.2+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ivar Vcs-Git: https://salsa.debian.org/med-team/ivar.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), libhts-dev Package-List: ivar deb science optional arch=any ivar-doc deb doc optional arch=all Checksums-Sha1: 8424d860241b5fdb7cfbb71d8d8d85d6d9162962 672788 ivar_1.4.2+dfsg.orig.tar.xz 3c8e54454b0d7d0870d99a6a746dfc8c302980ce 46324 ivar_1.4.2+dfsg-3.debian.tar.xz Checksums-Sha256: 87fbc667080e95823734eeca0dfcec058ff18f1aca7aff89de7a82217a7d2968 672788 ivar_1.4.2+dfsg.orig.tar.xz ea91d32c705d08f6397c9234d3d127f7be201c2c176be4aa83e4f72b76363ab0 46324 ivar_1.4.2+dfsg-3.debian.tar.xz Files: d2c0875cd8d094e11207d0d185099282 672788 ivar_1.4.2+dfsg.orig.tar.xz 7b90003c4369da383c9942994b2e1f9c 46324 ivar_1.4.2+dfsg-3.debian.tar.xz Dgit: cc92e3dc269b4f24682dfdaf04695cfc210a8aef debian archive/debian/1.4.2+dfsg-3 https://git.dgit.debian.org/ivar -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVvPnsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqrRg//RuzxRvOd8zpP3SzVppDe33LrwziH 38YnxXtMC5AMGDbUIgJSYCyynw3QqfgIA/j2SXHXjf2eizG/btaMBACvbnHJhifN Jy+iDNFeN9CqA8Lsq5seQIBKAOqXt2wcuRQvgt5/d3K3Y8wD8XYQ6p5wsbZNChbR TbpSfSQLo42NuXhugPi5sdis1mFFuS0eTcWHP0wi+/QwHJKNBKNTnMkd9N7vT2F7 1Rt4Kcjo8zFkUeISbp9Wm24fUTCyNH+SghBxdChhTaLiOgK5xZ4mA1UO5aj2vhKG dFSLUhzvylwNjgaty2IRFAVixdmngKmxZbX1c56GmfPqKWv2q5/iZC08+bKm3vXH 5zCZLEc5rpt3tukk8ihudm3M2BkZ3Avv4MkNACNQSSPGjhqornk5HbN5lOhPGoR2 VeUaufnhPuLOOPn5JLJs82QTGI9ihvvkfqnhYZAjYw3iImY1Binvp5mEPDKIpwAg OAcxifshzNYiIFfZri6XwjfimbLj/i+z28xUgGXycZLfBSvXJsKrHF/4cMxtgeKo FtsS8rCSEyaH+ZuTPu+sr5RTmvIEMsueupaARufs7V14xI3UFxLiLiLH48+x4JkM X792k9BQMVj42wyC6AUxzfBX2WmS4Udsh3egj9LX57C3MBm17SiCG6PKFUVmdbEc 8O4MaQ869zd8H2c= =3cR5 -----END PGP SIGNATURE----- Thu May 16 18:56:44 UTC 2024 I: Checking whether the package is not for us Thu May 16 18:56:44 UTC 2024 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net. Thu May 16 18:56:44 UTC 2024 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net. Thu May 16 18:59:42 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 16 06:56:50 -12 2024 I: pbuilder-time-stamp: 1715885810 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 [ivar_1.4.2+dfsg-3.dsc] I: copying [./ivar_1.4.2+dfsg.orig.tar.xz] I: copying [./ivar_1.4.2+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 5 15:15:07 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.2+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting ivar in ivar-1.4.2+dfsg dpkg-source: info: unpacking ivar_1.4.2+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.4.2+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix-warning.patch dpkg-source: info: applying forward-build-options.patch dpkg-source: info: applying privacy-breach.patch dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying gcc-13-2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21619/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='f5748ecab8fb414087738b731c5865a6' 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='21619' 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.zlRKWzZ1/pbuilderrc_wRGR --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.zlRKWzZ1/b1 --logfile b1/build.log ivar_1.4.2+dfsg-3.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64z 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 14 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/21619/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: armhf 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), libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19445 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 libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: 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} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx publicsuffix wget 0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 23.8 MB of archives. After unpacking 81.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1~rc2-1 [21.8 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 36 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.61.0-1+b1 [64.1 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-4.1+b2 [198 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.7.1-5 [385 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.7.1-5 [499 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1 [904 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1.1+b1 [1598 kB] Fetched 23.8 MB in 1s (46.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19445 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_armhf.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../22-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ivar-1.4.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ivar_1.4.2+dfsg-3_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.4.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:12: installing './compile' configure.ac:58: installing './config.guess' configure.ac:58: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 gawk... (cached) mawk 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 how to run the C preprocessor... gcc -E checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... no 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 unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for GNU libc compatible malloc... no checking for GNU libc compatible realloc... no checking for memmove... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg' Making all in src make[3]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Using built-in specs. Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --withUsing built-in specs. -target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --withCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc2TZGZn.s -target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc2qLROM.s Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-securityGNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Wall -Wextra -Werrorignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" -fstack-protector-strong -fstack-clash-protection -o /tmp/ccJOjSOU.s ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'alignment.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'ivar.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'call_consensus_pileup.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccBjqGqL.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'suffix_tree.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccIBBQmw.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccBjqGqL.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'remove_reads_from_amplicon.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o trim_primer_quality.o /tmp/ccNJVVq7.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'trim_primer_quality.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'call_variants.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccJBNFwe.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'primer_bed.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccTQFRPk.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' 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'-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'allele_functions.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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'-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccf6iBWY.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o get_masked_amplicons.o /tmp/ccJBNFwe.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'get_masked_amplicons.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccZX0bF5.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o get_common_variants.o /tmp/ccTQFRPk.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'get_common_variants.' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' /usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D _TIME_BITS=64 -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+fp -march=armv7-a+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccEvtDzp.s GNU C++17 (Debian 13.2.0-24) version 13.2.0 (arm-linux-gnueabihf) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/arm-linux-gnueabihf/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/arm-linux-gnueabihf/13/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. Compiler executable checksum: d88ac4b29a97bcb09bd584f88b5c1705 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o interval_tree.o /tmp/ccEvtDzp.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'interval_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o ref_seq.o /tmp/ccZX0bF5.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'ref_seq.' In file included from /usr/include/c++/13/regex:59, from parse_gff.h:6, from parse_gff.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/regex:57: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’, inlined from ‘std::vector gff3::query_features(uint64_t, std::string)’ at parse_gff.cpp:151:20: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘int gff3::read_file(std::string)’ at parse_gff.cpp:139:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a+fp -mfloat-abi=hard -meabi=5 -o parse_gff.o /tmp/ccf6iBWY.s GNU assembler version 2.42 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.42 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' '_TIME_BITS=64' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'parse_gff.' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/13/lto-wrapper Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-24' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a+fp --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Debian 13.2.0-24) MAKEFLAGS=w -j3 COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'ivar.' /usr/libexec/gcc/arm-linux-gnueabihf/13/collect2 -plugin /usr/libexec/gcc/arm-linux-gnueabihf/13/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/arm-linux-gnueabihf/13/lto-wrapper -plugin-opt=-fresolution=/tmp/ccw3Jy0u.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -dynamic-linker /lib/ld-linux-armhf.so.3 -X --hash-style=gnu --as-needed -m armelf_linux_eabi -pie -o ivar /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/Scrt1.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+fp' '-march=armv7-a+fp' '-dumpdir' 'ivar.' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/src' Making all in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg' dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg' Making check in src make[3]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/src' Making check in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold make[4]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp In file included from /usr/include/c++/13/regex:59, from ../src/parse_gff.h:6, from ../src/parse_gff.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/regex:57: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’, inlined from ‘std::vector gff3::query_features(uint64_t, std::string)’ at ../src/parse_gff.cpp:151:20: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘int gff3::read_file(std::string)’ at ../src/parse_gff.cpp:139:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_insert_threshold.o test_consensus_min_insert_threshold.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_insert_threshold test_consensus_min_insert_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread make[4]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[5]: Entering directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim PASS: check_consensus PASS: check_allele_depth PASS: check_consensus_threshold PASS: check_consensus_min_depth PASS: check_consensus_seq_id PASS: check_primer_bed PASS: check_getmasked PASS: check_removereads PASS: check_variants PASS: check_common_variants FAIL: check_unpaired_trim PASS: check_primer_trim_edge_cases PASS: check_isize_trim PASS: check_interval_tree PASS: check_amplicon_search PASS: check_consensus_min_insert_threshold ====================================== ivar 1.4.2: tests/test-suite.log ====================================== # TOTAL: 19 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: check_unpaired_trim ========================= Found 8 primers in BED file test_72_280_12:1:0_11:0:0_2 Forward Reverse Condensing cigar ... test_92_337_8:0:0_10:0:0_21 Forward Reverse Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65 Condensing cigar ... Cigar length didn't match after condense! Expected 19 Got 75 Cigar length didn't match after condense! Expected 56 Got 6 Cigar length didn't match after condense! Expected 1 Got 3 Cigar length didn't match after condense! Expected 6 Got 99 Cigar length didn't match after condense! Expected 3 Got 2 Cigar length didn't match after condense! Expected 99 Got 65 test_147_337_11:1:0_11:1:0_11 Forward Reverse Condensing cigar ... test_149_298_7:0:0_11:0:0_d Forward Reverse Condensing cigar ... test_184_379_11:1:0_8:1:0_26 Forward Reverse Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89 Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18 Condensing cigar ... Cigar length didn't match after condense! Expected 71 Got 160 Cigar flag didn't match! Expected  Got 4 Cigar length didn't match after condense! Expected 2 Got 18 FAIL check_unpaired_trim (exit status: 255) ============================================================================ Testsuite summary for ivar 1.4.2 ============================================================================ # TOTAL: 19 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log Please report to gkarthik@scripps.edu ============================================================================ make[5]: *** [Makefile:931: test-suite.log] Error 1 make[5]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[4]: *** [Makefile:1039: check-TESTS] Error 2 make[4]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[3]: *** [Makefile:1238: check-am] Error 2 make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg/tests' make[2]: *** [Makefile:371: check-recursive] Error 1 make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg' dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.2+dfsg' make: *** [debian/rules:12: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/21619 and its subdirectories Thu May 16 18:59:45 UTC 2024 W: No second build log, what happened?