https://launchpad.net/ubuntu/+source/ivar/1.4.2+dfsg-2ubuntu1/+build/26752088 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-079 5.4.0-163-generic #180-Ubuntu SMP Tue Sep 5 13:21:23 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 4 Oct 11:46:50 ntpdate[1858]: adjust time server 10.131.248.1 offset 0.001972 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26752088 --image-type chroot /home/buildd/filecache-default/03f085f954a1a101991fea4a2f82f6319e8baca5 Creating target for build PACKAGEBUILD-26752088 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26752088 Starting target for build PACKAGEBUILD-26752088 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26752088 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26752088 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26752088 Updating target for build PACKAGEBUILD-26752088 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1406 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [14.8 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5951 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [69.3 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [17.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [61.3 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [39.3 kB] Fetched 23.4 MB in 2s (9555 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev libgcrypt20 linux-libc-dev 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8156 kB of archives. After this operation, 1154 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libc6-dev amd64 2.38-1ubuntu6 [2113 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libc-dev-bin amd64 2.38-1ubuntu6 [20.3 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 linux-libc-dev amd64 6.5.0-7.7 [1562 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libc6 amd64 2.38-1ubuntu6 [3248 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libc-bin amd64 2.38-1ubuntu6 [680 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.2-3ubuntu1 [532 kB] Preconfiguring packages ... Fetched 8156 kB in 0s (79.7 MB/s) (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.38-1ubuntu6_amd64.deb ... Unpacking libc6-dev:amd64 (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.38-1ubuntu6_amd64.deb ... Unpacking libc-dev-bin (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Preparing to unpack .../linux-libc-dev_6.5.0-7.7_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.5.0-7.7) over (6.5.0-5.5) ... Preparing to unpack .../libc6_2.38-1ubuntu6_amd64.deb ... Unpacking libc6:amd64 (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Setting up libc6:amd64 (2.38-1ubuntu6) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../libc-bin_2.38-1ubuntu6_amd64.deb ... Unpacking libc-bin (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Setting up libc-bin (2.38-1ubuntu6) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.2-3ubuntu1_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.2-3ubuntu1) over (1.10.2-2ubuntu1) ... Setting up libgcrypt20:amd64 (1.10.2-3ubuntu1) ... Setting up linux-libc-dev:amd64 (6.5.0-7.7) ... Setting up libc-dev-bin (2.38-1ubuntu6) ... Setting up libc6-dev:amd64 (2.38-1ubuntu6) ... Processing triggers for libc-bin (2.38-1ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26752088 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26752088 --arch=amd64 --dist=mantic-proposed --nolog -A ivar_1.4.2+dfsg-2ubuntu1.dsc Initiating build PACKAGEBUILD-26752088 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-163-generic #180-Ubuntu SMP Tue Sep 5 13:21:23 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-079.buildd +==============================================================================+ | ivar 1.4.2+dfsg-2ubuntu1 (amd64) Wed, 04 Oct 2023 11:47:01 +0000 | +==============================================================================+ Package: ivar Version: 1.4.2+dfsg-2ubuntu1 Source Version: 1.4.2+dfsg-2ubuntu1 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26752088/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/ivar-SNKUQQ/resolver-1U64p2' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ivar_1.4.2+dfsg-2ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/ivar-SNKUQQ/ivar-1.4.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/ivar-SNKUQQ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libhts-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [377 B] Get:5 copy:/<>/apt_archive ./ Packages [462 B] Fetched 1796 B in 0s (133 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After this operation, 89.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [670 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libelf1 amd64 0.189-4 [56.3 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu3 [10.8 MB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [764 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext-base amd64 0.21-13 [38.1 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 groff-base amd64 1.23.0-2 [1023 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 libnghttp2-14 amd64 1.55.1-1 [72.8 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 libpsl5 amd64 0.21.2-1 [59.0 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 man-db amd64 2.11.2-3 [1220 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 autopoint all 0.21-13 [422 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebhelper-perl all 13.11.6ubuntu1 [85.4 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libtool all 2.4.7-7 [166 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 libdw1 amd64 0.189-4 [257 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext amd64 0.21-13 [866 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 debhelper all 13.11.6ubuntu1 [935 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libbrotli1 amd64 1.0.9-2build8 [309 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-3 [20.2 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-3 [53.4 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libldap2 amd64 2.6.6+dfsg-1~exp1ubuntu1 [193 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libssh-4 amd64 0.10.5-3ubuntu1 [187 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl3-gnutls amd64 8.2.1-1ubuntu3 [312 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4-gnutls-dev amd64 8.2.1-1ubuntu3 [420 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libdeflate0 amd64 1.18-1 [43.1 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 libdeflate-dev amd64 1.18-1 [49.8 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhtscodecs2 amd64 1.5.1-1 [96.7 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhts3 amd64 1.17+ds-1 [429 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma-dev amd64 5.4.1-0.2 [177 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu5 [895 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhts-dev amd64 1.17+ds-1 [5756 kB] Preconfiguring packages ... Fetched 28.0 MB in 0s (108 MB/s) Selecting previously unselected package libelf1:amd64. (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.189-4_amd64.deb ... Unpacking libelf1:amd64 (0.189-4) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../01-libicu72_72.1-3ubuntu3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3ubuntu3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. 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Unpacking libhts-dev:amd64 (1.17+ds-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../47-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.5.1-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3ubuntu3) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.6ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build8) ... Setting up libnghttp2-14:amd64 (1.55.1-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up gettext-base (0.21-13) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up autopoint (0.21-13) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Setting up libssh-4:amd64 (0.10.5-3ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libdeflate-dev:amd64 (1.18-1) ... Setting up libelf1:amd64 (0.189-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... Setting up libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.189-4) ... Setting up gettext (0.21-13) ... Setting up libtool (2.4.7-7) ... Setting up libcurl3-gnutls:amd64 (8.2.1-1ubuntu3) ... Setting up libcurl4-gnutls-dev:amd64 (8.2.1-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-2) ... Setting up debugedit (1:5.0-5) ... Setting up libhts3:amd64 (1.17+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.17+ds-1) ... Setting up man-db (2.11.2-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up debhelper (13.11.6ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-1ubuntu6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-163-generic #180-Ubuntu SMP Tue Sep 5 13:21:23 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.41-5ubuntu1 dpkg-dev_1.22.0ubuntu1 g++-13_13.2.0-4ubuntu3 gcc-13_13.2.0-4ubuntu3 libc6-dev_2.38-1ubuntu6 libstdc++-13-dev_13.2.0-4ubuntu3 libstdc++6_13.2.0-4ubuntu3 linux-libc-dev_6.5.0-7.7 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 apt-utils_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 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init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-3ubuntu1 libacl1_2.3.1-3 libapparmor1_4.0.0~alpha2-0ubuntu5 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.2.0-4ubuntu3 libassuan0_2.5.6-1 libatomic1_13.2.0-4ubuntu3 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-5ubuntu1 libblkid1_2.39.1-4ubuntu1 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-1ubuntu6 libc-dev-bin_2.38-1ubuntu6 libc6_2.38-1ubuntu6 libc6-dev_2.38-1ubuntu6 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-4ubuntu3 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-4ubuntu3 libctf-nobfd0_2.41-5ubuntu1 libctf0_2.41-5ubuntu1 libcurl3-gnutls_8.2.1-1ubuntu3 libcurl4-gnutls-dev_8.2.1-1ubuntu3 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.6ubuntu1 libdeflate-dev_1.18-1 libdeflate0_1.18-1 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------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.4.2+dfsg-2ubuntu1 Maintainer: Ubuntu Developers Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ivar Vcs-Git: https://salsa.debian.org/med-team/ivar.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), libhts-dev Package-List: ivar deb science optional arch=any ivar-doc deb doc optional arch=all Checksums-Sha1: 8424d860241b5fdb7cfbb71d8d8d85d6d9162962 672788 ivar_1.4.2+dfsg.orig.tar.xz 3168ebb0067dfae76b6c9f85d1c0f43efe3fd19f 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Checksums-Sha256: 87fbc667080e95823734eeca0dfcec058ff18f1aca7aff89de7a82217a7d2968 672788 ivar_1.4.2+dfsg.orig.tar.xz 3fec41e1a67e7670c7cff180ff5e565a59f1240c9603a6642b2a3c3e1f2f7c12 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Files: d2c0875cd8d094e11207d0d185099282 672788 ivar_1.4.2+dfsg.orig.tar.xz d5eb0ed55db68fff481c6bb5471aaba5 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmUdT+YACgkQr8/sjmac 4cLEhg/+LHuBmMW1Ol8i1nfV2yWMvUO45FeCWDjjm9unp4WBww6mE97CVyBQG1Re Df7jEk1fCsGH3T/CgqKZedgkkNNQeWVZfPR/KZ4UIZgizcIWKl8r0JwTBGP0YkYD c4bC1DkTlGfhCn+h5QstHC+hClOqxyU0Oyy8aVjEuMKKmRHnzUBF0pH/B1ND/vLP BepRRAady1HRlnqIlIRZyMbqmgSeLRKzHKpvMiF75qfwbsuEVanneBeL34rnUbLi wz0XU0p7S7TCAsnPiUYTbqpzz5nC4rFiqYCKAZerFxARjjdU3jLxNZdbnGZJ3Uok T6QCkrDvwXrcFrNYxPWY/kdIrG9v/FPFbIe+UTcMePPPW4/3C14yIbb8sWH/L3tv ExpByLz4JVZF2o6hQDuHKXoMg3F7QCAuZ9jnwJX0HjS8DJLOUzTs8JcxUYVDS6uP EUMqeceEgYIKwexMDmO50Inoa2K1VVvd+c29pgKOo64Pf1K99flkbXFY+U6Zyimp LDXy1Jc1LT/YAf/8+sUh+ifPX531IWg3UeNxVTIdbosgP+w8ujN5uzNtTUG3KRX0 lHw7wxY1SsAM6LaT3gudux0NX1LVzN7YrdpvMry8HcAOySMmSAv5ddGu6vksNGj9 eP8NE/Iw/JjMK2VFPaG62qO2Mjwo/ENnb/Ng5JAR4b26OhUqS8E= =qDfj -----END PGP SIGNATURE----- gpgv: Signature made Wed Oct 4 11:43:34 2023 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.2+dfsg-2ubuntu1.dsc: no acceptable signature found dpkg-source: info: extracting ivar in /<> dpkg-source: info: unpacking ivar_1.4.2+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.4.2+dfsg-2ubuntu1.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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26752088 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26752088 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26752088 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.4.2+dfsg-2ubuntu1 dpkg-buildpackage: info: source distribution mantic dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai make[1]: Leaving directory '/<>' 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... 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 -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in src make[3]: Entering directory '/<>/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp Using built-in specs. 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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/ccG31jQc.s GNU assembler version 2.41 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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/ccuSJIrz.s GNU assembler version 2.41 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_masked_amplicons.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: 2d107d43320bae9d835c0808be5fcba6 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_common_variants.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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/cczZPOKm.s GNU assembler version 2.41 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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/cctcFpkN.s GNU assembler version 2.41 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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/ccVa1CZE.s GNU assembler version 2.41 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -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/13/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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) MAKEFLAGS=w -j4 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' /usr/libexec/gcc/x86_64-linux-gnu/13/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/13/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper -plugin-opt=-fresolution=/tmp/ccnMWqr2.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 -z now -z relro -o ivar /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../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/13/../../.. -Bsymbolic-functions -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/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Leaving directory '/<>/src' Making all in tests make[3]: Entering directory '/<>/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/<>' Making check in src make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src' Making check in tests make[3]: Entering directory '/<>/tests' make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold make[4]: Entering directory '/<>/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -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. 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'/<>/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 ============================================================================ Testsuite summary for ivar 1.4.2 ============================================================================ # TOTAL: 19 # PASS: 19 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering 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COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/13/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='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=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-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/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/gcc-13-13.2.0/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=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) MAKEFLAGS=w -j4 -- DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' /usr/libexec/gcc/x86_64-linux-gnu/13/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/13/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper -plugin-opt=-fresolution=/tmp/ccyV0ekc.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 -z now -z relro -o ivar /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../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/13/../../.. -Bsymbolic-functions -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/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ivar '/<>/debian/tmp/usr/bin' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making install in tests make[2]: Entering directory '/<>/tests' make[3]: Entering directory '/<>/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 '/<>/tests' make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a f1498b4d734c6e68f14ece3b80d26f437a111e4f dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ivar-doc (in debian/ivar-doc); do_strip: , oemstrip: pkgstriptranslations: processing ivar (in debian/ivar); do_strip: , oemstrip: pkgstriptranslations: processing ivar-dbgsym (in debian/.debhelper/ivar/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/ivar-doc/DEBIAN/control, package ivar-doc, directory debian/ivar-doc INFO: pkgstripfiles: waiting for lock (ivar-doc) ... pkgstripfiles: processing control file: debian/ivar/DEBIAN/control, package ivar, directory debian/ivar pkgstripfiles: Truncating usr/share/doc/ivar/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package ivar ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ivar' in '../ivar_1.4.2+dfsg-2ubuntu1_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/ivar/dbgsym-root/DEBIAN/control, package ivar-dbgsym, directory debian/.debhelper/ivar/dbgsym-root dpkg-deb: building package 'ivar-dbgsym' in 'debian/.debhelper/scratch-space/build-ivar/ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.deb'. Renaming ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.deb to ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb pkgstripfiles: Truncating usr/share/doc/ivar-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package ivar-doc (to save build time) dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb'. dpkg-genbuildinfo --build=binary -O../ivar_1.4.2+dfsg-2ubuntu1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../ivar_1.4.2+dfsg-2ubuntu1_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) -------------------------------------------------------------------------------- Build finished at 2023-10-04T11:48:01Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ivar_1.4.2+dfsg-2ubuntu1_amd64.changes: --------------------------------------- Format: 1.8 Date: Wed, 27 Sep 2023 12:41:50 -0300 Source: ivar Binary: ivar ivar-doc Built-For-Profiles: noudeb Architecture: amd64 all Version: 1.4.2+dfsg-2ubuntu1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Mateus Rodrigues de Morais Description: ivar - functions broadly useful for viral amplicon-based sequencing ivar-doc - functions broadly useful for viral amplicon-based sequencing (doc Launchpad-Bugs-Fixed: 2037769 Changes: ivar (1.4.2+dfsg-2ubuntu1) mantic; urgency=medium . * d/rules: disable LTO to fix failure to build from source on amd64 and arm64 on Ubuntu. (LP: #2037769) Checksums-Sha1: 86795d5030f522f7e843cd5995ec4e9c88921603 1707442 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb dd6b572dede075265a8dce17e39f5400b352b558 257270 ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb 293eae208e99dab43c30136dc1384f6a77c3ff57 6694 ivar_1.4.2+dfsg-2ubuntu1_amd64.buildinfo 40a559b81faa79b2441cff11abd879ac790dc382 237012 ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Checksums-Sha256: 8716e42bdeba8a3842363f0474952c21aa871c4e2bb994e228f99193d6efdd28 1707442 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb 20c71f9697f5c5cf2b2ce3759d4733cc737928b80ba336f4baef52fdbbcef152 257270 ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb c3754a179b7641956bdccbed32e16e34b594b3099b1e71b0f490d23600003b7d 6694 ivar_1.4.2+dfsg-2ubuntu1_amd64.buildinfo 17b83aaea24f9c1c3b60607663615951e7e47204a7392af04f93862f16fa40a8 237012 ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Files: 3ae9449970655b23fc9f3437e9250e6b 1707442 debug optional ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb 7fe9aeeed61a5576408e79da36ce6c4a 257270 doc optional ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb 2537891676013bdf2afa9ed2fc7bd4aa 6694 science optional ivar_1.4.2+dfsg-2ubuntu1_amd64.buildinfo c9cc5ccd5d650f46b6c2f03834e1ed1b 237012 science optional ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Original-Maintainer: Debian Med Packaging Team /<>/ivar_1.4.2+dfsg-2ubuntu1_amd64.changes.new could not be renamed to /<>/ivar_1.4.2+dfsg-2ubuntu1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: ivar Binary: ivar ivar-dbgsym ivar-doc Architecture: all amd64 Version: 1.4.2+dfsg-2ubuntu1 Checksums-Md5: 3ae9449970655b23fc9f3437e9250e6b 1707442 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb 7fe9aeeed61a5576408e79da36ce6c4a 257270 ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb c9cc5ccd5d650f46b6c2f03834e1ed1b 237012 ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Checksums-Sha1: 86795d5030f522f7e843cd5995ec4e9c88921603 1707442 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb dd6b572dede075265a8dce17e39f5400b352b558 257270 ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb 40a559b81faa79b2441cff11abd879ac790dc382 237012 ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Checksums-Sha256: 8716e42bdeba8a3842363f0474952c21aa871c4e2bb994e228f99193d6efdd28 1707442 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_amd64.ddeb 20c71f9697f5c5cf2b2ce3759d4733cc737928b80ba336f4baef52fdbbcef152 257270 ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb 17b83aaea24f9c1c3b60607663615951e7e47204a7392af04f93862f16fa40a8 237012 ivar_1.4.2+dfsg-2ubuntu1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Wed, 04 Oct 2023 11:48:01 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.41-5ubuntu1), binutils-common (= 2.41-5ubuntu1), binutils-x86-64-linux-gnu (= 2.41-5ubuntu1), bsdextrautils (= 2.39.1-4ubuntu1), bsdutils (= 1:2.39.1-4ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:13.2.0-1ubuntu1), cpp-13 (= 13.2.0-4ubuntu3), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.6ubuntu1), debianutils (= 5.8-1), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.22.0ubuntu1), dpkg-dev (= 1.22.0ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1ubuntu1), g++-13 (= 13.2.0-4ubuntu3), gcc (= 4:13.2.0-1ubuntu1), gcc-13 (= 13.2.0-4ubuntu3), gcc-13-base (= 13.2.0-4ubuntu3), gettext (= 0.21-13), gettext-base (= 0.21-13), grep (= 3.11-2), groff-base (= 1.23.0-2), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-4ubuntu3), libatomic1 (= 13.2.0-4ubuntu3), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-5ubuntu1), libblkid1 (= 2.39.1-4ubuntu1), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-1ubuntu6), libc-dev-bin (= 2.38-1ubuntu6), libc6 (= 2.38-1ubuntu6), libc6-dev (= 2.38-1ubuntu6), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-4ubuntu3), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-5ubuntu1), libctf0 (= 2.41-5ubuntu1), libcurl3-gnutls (= 8.2.1-1ubuntu3), libcurl4-gnutls-dev (= 8.2.1-1ubuntu3), libdb5.3 (= 5.3.28+dfsg2-2), libdebconfclient0 (= 0.270ubuntu1), libdebhelper-perl (= 13.11.6ubuntu1), libdeflate-dev (= 1.18-1), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.0ubuntu1), libdw1 (= 0.189-4), libelf1 (= 0.189-4), libffi8 (= 3.4.4-1), 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2.39.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.55.1-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.25.0-4ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9ubuntu1), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), libquadmath0 (= 13.2.0-4ubuntu3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-3), libsasl2-modules-db (= 2.1.28+dfsg1-3), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.5-1), libsframe1 (= 2.41-5ubuntu1), libsmartcols1 (= 2.39.1-4ubuntu1), libssh-4 (= 0.10.5-3ubuntu1), libssl3 (= 3.0.10-1ubuntu2), libstdc++-13-dev (= 13.2.0-4ubuntu3), libstdc++6 (= 13.2.0-4ubuntu3), libsub-override-perl (= 0.09-4), libsystemd0 (= 253.5-1ubuntu6), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20230625-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-4ubuntu3), libubsan1 (= 13.2.0-4ubuntu3), libuchardet0 (= 0.0.7-1build2), libudev1 (= 253.5-1ubuntu6), libunistring2 (= 1.0-2), libuuid1 (= 2.39.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-1ubuntu2), linux-libc-dev (= 6.5.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 43), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-3), mawk (= 1.3.4.20230730-1), ncurses-base (= 6.4+20230625-2), ncurses-bin (= 6.4+20230625-2), patch (= 2.7.6-7build2), perl (= 5.36.0-9ubuntu1), perl-base (= 5.36.0-9ubuntu1), perl-modules-5.36 (= 5.36.0-9ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.07-1ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), util-linux (= 2.39.1-4ubuntu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu5), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu5) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1695829310" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ivar-doc_1.4.2+dfsg-2ubuntu1_all.deb ------------------------------------ new Debian package, version 2.0. size 257270 bytes: control archive=4665 bytes. 1275 bytes, 28 lines control 12213 bytes, 156 lines md5sums Package: ivar-doc Source: ivar Version: 1.4.2+dfsg-2ubuntu1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 1180 Depends: node-jquery Section: doc Priority: optional Multi-Arch: foreign Homepage: https://github.com/andersen-lab/ivar Description: functions broadly useful for viral amplicon-based sequencing (documentation) iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. iVar provided the following functions: . 1. trimming of primers and low-quality bases, 2. consensus calling, 3. variant calling - both iSNVs and insertions/deletions, and 4. identifying mismatches to primer sequences and excluding the corresponding reads from alignment files. . This package contains the html documentation for ivar. 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237012 bytes: control archive=2428 bytes. 1255 bytes, 25 lines control 4870 bytes, 58 lines md5sums Package: ivar Version: 1.4.2+dfsg-2ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 1518 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3 (>= 1.17), libstdc++6 (>= 13.1) Recommends: samtools Section: science Priority: optional Homepage: https://github.com/andersen-lab/ivar Description: functions broadly useful for viral amplicon-based sequencing iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. iVar provided the following functions: . 1. trimming of primers and low-quality bases, 2. consensus calling, 3. variant calling - both iSNVs and insertions/deletions, and 4. identifying mismatches to primer sequences and excluding the corresponding reads from alignment files. 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+------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 60728 Build-Time: 53 Distribution: mantic-proposed Host Architecture: amd64 Install-Time: 6 Job: ivar_1.4.2+dfsg-2ubuntu1.dsc Machine Architecture: amd64 Package: ivar Package-Time: 60 Source-Version: 1.4.2+dfsg-2ubuntu1 Space: 60728 Status: successful Version: 1.4.2+dfsg-2ubuntu1 -------------------------------------------------------------------------------- Finished at 2023-10-04T11:48:01Z Build needed 00:01:00, 60728k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26752088 Scanning for processes to kill in build PACKAGEBUILD-26752088