Fri Nov 22 02:22:11 UTC 2024 I: starting to build ivar/trixie/amd64 on jenkins on '2024-11-22 02:21' Fri Nov 22 02:22:11 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/38210/console.log Fri Nov 22 02:22:11 UTC 2024 I: Downloading source for trixie/ivar=1.4.3+dfsg-2 --2024-11-22 02:22:11-- http://deb.debian.org/debian/pool/main/i/ivar/ivar_1.4.3%2bdfsg-2.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_1.4.3+dfsg-2.dsc’ 0K .. 100% 294M=0s 2024-11-22 02:22:11 (294 MB/s) - ‘ivar_1.4.3+dfsg-2.dsc’ saved [2205/2205] Fri Nov 22 02:22:11 UTC 2024 I: ivar_1.4.3+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.4.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.7.0 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: b3321b88507ca2939854142a4b8a211b8f718ff3 674816 ivar_1.4.3+dfsg.orig.tar.xz a0301ce9286b8b5063a5b90de79c015c4e171d51 46396 ivar_1.4.3+dfsg-2.debian.tar.xz Checksums-Sha256: 262c15f5135207598785d3eb29698d4a0534c029408c917d18efb1ebc167d41f 674816 ivar_1.4.3+dfsg.orig.tar.xz 6b534b45e30e06667f6b1922934cc6aa588535d871a20336c0e42d7868d4b718 46396 ivar_1.4.3+dfsg-2.debian.tar.xz Files: bb436c8709f7f188433296aef15b41ee 674816 ivar_1.4.3+dfsg.orig.tar.xz 388f2a5bd860349586e3513d912ac57d 46396 ivar_1.4.3+dfsg-2.debian.tar.xz Dgit: 1a804969f3ffe3f2a3f77987f498d009f8fcf8a3 debian archive/debian/1.4.3+dfsg-2 https://git.dgit.debian.org/ivar -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmaToY0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrFQg//foNli4YAPSpaLzp5yRutpsW9/1sa rKCDhji+0yxMs3OdL9jLCWRK7KMCFNcRwXQp+SDAJtL0YWbXBLZPo5KmxV7AUTAX a/IgPYEZO67shNRGArIT9N2HK5qKtfbd+Un93iQTX44vIesmQEFUQ1hVzc8RYX8K 3niriU9Yv+Rnh5cFZ3B53L7Zr19bjGerLokrCZEKD5Y4ApyIa5wt848QNxSEaMvH /cbjydcrDCyhbcBJD5hdHxxABknpwJOsQc1uzoJcqmdsOkVwkahZz2ZQ/jpISsMp NN6A7HEPgmfoY01oyP4QS0OTNvgnsGCaZwpiVWkesUiaOepAuIK/jgrdly1IDiOg yF1Xfz3Ecm6EgXmBh7fWSH9IjJ9Wk9rc3HiqCrxDgFtilMSGA/RQ2WAFJoptFhmS OM557zcdNLGCb4ydlRsMT6q3nA2okK0UDxqbGH0ROwrpV8QpJjHvBKwXmPHi2wrF sTM3iET17owz83z5qX9vqx1tuJUhpdxw5Av/pYafIZDCozTid2QONmevoti6ZRFC R6o/LFoF+DPo1gZk5pD7H0ruZwCpa+pqx5ruDn96sxvXIqCI4InHKdJ7dgGjFjSE 0vFV4FVsFS5QIe4dhv9B6q/eih5NgESLKKKHpl6j9yZHFu662MKH3c9SLbTZb5wW 7g/VpG4zTUtKot8= =WWVS -----END PGP SIGNATURE----- Fri Nov 22 02:22:11 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 02:22:11 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Nov 22 02:22:11 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Nov 22 02:23:36 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 20:45:13 -12 2025 I: pbuilder-time-stamp: 1766652313 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_1.4.3+dfsg-2.dsc] I: copying [./ivar_1.4.3+dfsg.orig.tar.xz] I: copying [./ivar_1.4.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jul 14 09:59:41 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting ivar in ivar-1.4.3+dfsg dpkg-source: info: unpacking ivar_1.4.3+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.4.3+dfsg-2.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/3408315/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5e8bd6e4f2b14c5da8670b681e9e9f0e' 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='3408315' 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.xfDVDDJq/pbuilderrc_6bpx --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.xfDVDDJq/b1 --logfile b1/build.log ivar_1.4.3+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3408315/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19969 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 37.0 MB of archives. After unpacking 135 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.1-1+b1 [54.8 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.4.0-1+b1 [87.2 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Fetched 37.0 MB in 2s (24.4 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 ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.8-2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up comerr-dev:amd64 (2.1-1.47.1-1+b1) ... Setting up libssl-dev:amd64 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1+b1) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ivar-1.4.3+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_1.4.3+dfsg-2_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.4.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --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 or later... 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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 -j42 make[1]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' Making all in src make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp Using built-in specs. g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -oUsing built-in specs. /tmp/ccmy5iOE.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus--enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/deb -quietian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-c -vuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-con -Ifig=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix .Supported LTO compression algorithms: zlib -I zstd .. -imultiarchgcc version 14.2.0 (Debian 14.2.0-8) x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccwVZDyW.s COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccq1WU4f.s Using built-in specs. g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccYmxiXP.s g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccXDAIzS.s g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cctRBtFC.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccvidb0o.s Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -WerrorUsing built-in specs. -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccsvwfQV.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map--program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format- --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enablesecurity' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=g-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-veeneric' '-march=x86-64' rify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus zstd -quiet -v -Igcc version 14.2.0 (Debian 14.2.0-8) . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccXXZpbS.s Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccLpxWyT.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto Using built-in specs. --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccnSTNOT.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccP2K6gp.s ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" Using built-in specs. ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: #include "..." search starts here: . #include <...> search starts here: .. . /usr/include/c++/14 .. /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14 /usr/include/c++/14/backward /usr/include/x86_64-linux-gnu/c++/14 /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/include/c++/14/backward /usr/local/include /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/include/x86_64-linux-gnu /usr/local/include /usr/include /usr/include/x86_64-linux-gnu End of search list. /usr/include End of search list. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debGNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, ian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP gcc version 14.2.0 (Debian 14.2.0-8) GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -vignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" -I .ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" -I ..ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D#include "..." search starts here: _FORTIFY_SOURCE=2#include <...> search starts here: ref_seq.cpp . -quiet .. /usr/include/c++/14 -dumpbase /usr/include/x86_64-linux-gnu/c++/14 ref_seq.cpp /usr/include/c++/14/backward -dumpbase-ext /usr/lib/gcc/x86_64-linux-gnu/14/include .cpp /usr/local/include /usr/include/x86_64-linux-gnu -mtune=generic /usr/include -march=x86-64End of search list. -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cchrDS4y.s COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mtune=genericGGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccFV2Uqm.s ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 #include "..." search starts here: /usr/include/x86_64-linux-gnu/c++/14 #include <...> search starts here: /usr/include/c++/14/backward . /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include .. /usr/include/x86_64-linux-gnu /usr/include/c++/14 /usr/include /usr/include/x86_64-linux-gnu/c++/14 End of search list. /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. Compiler executable checksum: GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, 61acd6GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP efe071b56ba22025963fbe8d32GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" 61acd6efe0ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" 71b56ba220ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" 25963fignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" be8d32ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 GNU C++17 (Debian 14.2.0-8) version 14.2.0 (x86_64-linux-gnu) compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/14 /usr/include/x86_64-linux-gnu/c++/14 /usr/include/c++/14/backward /usr/lib/gcc/x86_64-linux-gnu/14/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b5Compiler executable checksum: 6ba2206125ac96d6ef3fe0be71b58d6b32a2Compiler executable checksum: 20 256196ac3fd6beef8de03271b5 6ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 Compiler executable checksum: 61acd6efe071b56ba22025963fbe8d32 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o interval_tree.o /tmp/ccFV2Uqm.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'interval_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccq1WU4f.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/cctRBtFC.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o get_masked_amplicons.o /tmp/ccLpxWyT.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_masked_amplicons.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/ccXXZpbS.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o ref_seq.o /tmp/cchrDS4y.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o get_common_variants.o /tmp/ccnSTNOT.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'allele_functions.' MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ref_seq.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccvidb0o.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_common_variants.' MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccmy5iOE.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/ccsvwfQV.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccYmxiXP.s MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.' GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/ccwVZDyW.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccXDAIzS.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --gdwarf-5 --64 -o parse_gff.o /tmp/ccP2K6gp.s GNU assembler version 2.43.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.43.1 MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'parse_gff.' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) MAKEFLAGS=w -j42 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/cc6oUGtq.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 -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -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/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' Making all in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' Making check in src make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' Making check in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+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 check_quality_trim_unpaired check_strand_variants make[4]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/primer_bed.o ../src/primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_trim.o test_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_quality_trim.o test_quality_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -Wl,-z,relro -Wl,-z,now -o check_quality_trim test_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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_allele_depth.o test_allele_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_primer_bed.o test_primer_bed.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_getmasked.o test_getmasked.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_removereads.o test_removereads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_variants.o test_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/call_variants.o ../src/call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/parse_gff.o ../src/parse_gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_common_variants.o test_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_isize_trim.o test_isize_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_interval_tree.o test_interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_consensus_min_insert_threshold.o test_consensus_min_insert_threshold.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -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 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_quality_trim_unpaired.o test_quality_trim_unpaired.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -Wl,-z,relro -Wl,-z,now -o check_quality_trim_unpaired test_quality_trim_unpaired.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -c -o test_variants_reverse_strand.o test_variants_reverse_strand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wextra -Werror -Wno-unused-but-set-variable -Wl,-z,relro -Wl,-z,now -o check_strand_variants test_variants_reverse_strand.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread make[4]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[5]: Entering directory '/build/reproducible-path/ivar-1.4.3+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 PASS: 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 PASS: check_quality_trim_unpaired PASS: check_strand_variants ============================================================================ Testsuite summary for ivar 1.4.3 ============================================================================ # TOTAL: 21 # PASS: 21 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[4]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j42 install DESTDIR=/build/reproducible-path/ivar-1.4.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) MAKEFLAGS=w -j42 -- DESTDIR=/build/reproducible-path/ivar-1.4.3+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/ccQGEamf.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 -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -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/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.3+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/ivar-1.4.3+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ivar '/build/reproducible-path/ivar-1.4.3+dfsg/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/src' Making install in tests make[2]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg/tests' make[2]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[3]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules execute_before_dh_fixperms make[1]: Entering directory '/build/reproducible-path/ivar-1.4.3+dfsg' if [ -x /build/reproducible-path/ivar-1.4.3+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/data/primer_pair_test/test_primer_pair.bed ] \ ; then chmod -v -x /build/reproducible-path/ivar-1.4.3+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed \ ; fi make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.3+dfsg' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'ivar' in '../ivar_1.4.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.4.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.4.3+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../ivar_1.4.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../ivar_1.4.3+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3408315 and its subdirectories I: Current time: Wed Dec 24 20:46:35 -12 2025 I: pbuilder-time-stamp: 1766652395 Fri Nov 22 02:23:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Nov 22 02:23:37 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Nov 22 02:29:47 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Nov 22 02:29:48 UTC 2024 I: ivar_1.4.3+dfsg-2_amd64.changes: Format: 1.8 Date: Sun, 14 Jul 2024 11:40:01 +0200 Source: ivar Binary: ivar ivar-dbgsym ivar-doc Architecture: amd64 all Version: 1.4.3+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: ivar - functions broadly useful for viral amplicon-based sequencing ivar-doc - functions broadly useful for viral amplicon-based sequencing (doc Changes: ivar (1.4.3+dfsg-2) unstable; urgency=medium . * d/rules: fix arch-all build failure. Checksums-Sha1: ad153816afea6a086e4cbc9d2de77d462cd7fc84 1727108 ivar-dbgsym_1.4.3+dfsg-2_amd64.deb 470f0ead189f8517564682962549a7b7ee3c787e 254752 ivar-doc_1.4.3+dfsg-2_all.deb b370877e354d2985ec88412839e4d07fa3553ef4 7295 ivar_1.4.3+dfsg-2_amd64.buildinfo d549e01eadfbaefe471a9f227414a2a6f85b1e3c 229700 ivar_1.4.3+dfsg-2_amd64.deb Checksums-Sha256: 6c4b5408eaffc1d36ba783e0f860ac809a63559e783dbcb9020dde969be52e66 1727108 ivar-dbgsym_1.4.3+dfsg-2_amd64.deb b102da4f0bcb6628b681551a757fb5c8ff03f1b16b4a37fb66cf2cda249775e9 254752 ivar-doc_1.4.3+dfsg-2_all.deb a97cf332de8df480c23b136300871af017a22875278873cfe256ed037a3002ac 7295 ivar_1.4.3+dfsg-2_amd64.buildinfo c78533cec8526d257bbfa2ee80a333a63c82a2d1eac270c7676e031ed051fbc2 229700 ivar_1.4.3+dfsg-2_amd64.deb Files: 439679e37f093fa74e2c20107fbea49b 1727108 debug optional ivar-dbgsym_1.4.3+dfsg-2_amd64.deb 09bc80c775a7d040dbf4b03e21a7caf8 254752 doc optional ivar-doc_1.4.3+dfsg-2_all.deb 88d29e535c712ec6c0f0b55b20db1987 7295 science optional ivar_1.4.3+dfsg-2_amd64.buildinfo 1b3a4f419de98c2af370947d1221eb00 229700 science optional ivar_1.4.3+dfsg-2_amd64.deb Fri Nov 22 02:29:49 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_12-38210.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xfDVDDJq/ivar_1.4.3+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xfDVDDJq/ivar_1.4.3+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xfDVDDJq/ivar_1.4.3+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xfDVDDJq/b1/ivar_1.4.3+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xfDVDDJq/b2/ivar_1.4.3+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.359s) 0.359s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.041s) 0.041s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 697ms CPU time consumed: 696ms Fri Nov 22 02:29:50 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 02:29:50 UTC 2024 I: ivar from trixie built successfully and reproducibly on amd64. Fri Nov 22 02:29:51 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 02:29:51 UTC 2024 I: Submitting 8.0K b1/ivar_1.4.3+dfsg-2_amd64.buildinfo.asc Fri Nov 22 02:29:53 UTC 2024 I: Submitting 8.0K b2/ivar_1.4.3+dfsg-2_amd64.buildinfo.asc Fri Nov 22 02:29:53 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 02:29:53 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 02:29:53 UTC 2024 I: Removing signed ivar_1.4.3+dfsg-2_amd64.buildinfo.asc files: removed './b1/ivar_1.4.3+dfsg-2_amd64.buildinfo.asc' removed './b2/ivar_1.4.3+dfsg-2_amd64.buildinfo.asc'