https://launchpad.net/ubuntu/+source/hmmer2/2.3.2+dfsg-8/+build/24934573 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-010 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 13 Dec 11:38:24 ntpdate[1858]: adjust time server 10.211.37.1 offset -0.000919 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-24934573 --image-type chroot /home/buildd/filecache-default/0ff053c85babb2453d3b9b9b50ec5a50c26e70b3 Creating target for build PACKAGEBUILD-24934573 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-24934573 Starting target for build PACKAGEBUILD-24934573 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-24934573 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24934573 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-24934573 Updating target for build PACKAGEBUILD-24934573 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main arm64 Packages [1370 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe arm64 Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5866 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 Packages [131 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [49.0 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe arm64 Packages [1288 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [416 kB] Fetched 24.8 MB in 4s (6972 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: lsb-base* The following NEW packages will be installed: libjansson4 libperl5.36 perl-modules-5.36 The following packages will be upgraded: adduser binutils binutils-aarch64-linux-gnu binutils-common ca-certificates coreutils cpp-12 dash debconf dpkg dpkg-dev g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libbinutils libcap2 libcc1-0 libctf-nobfd0 libctf0 libdpkg-perl libgcc-12-dev libgcc-s1 libgomp1 libgprofng0 libhwasan0 libitm1 libkmod2 liblsan0 liblz4-1 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtsan2 libubsan1 libudev1 linux-libc-dev openssl perl perl-base systemd systemd-sysv sysvinit-utils zlib1g 47 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 80.4 MB of archives. After this operation, 53.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 coreutils arm64 9.1-1ubuntu1 [1347 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 dpkg arm64 1.21.12ubuntu2 [1346 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main arm64 dash arm64 0.5.11+git20210903+057cd650a4ed-9ubuntu1 [88.2 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl-modules-5.36 all 5.36.0-6 [2985 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libperl5.36 arm64 5.36.0-6 [4677 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl arm64 5.36.0-6 [235 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl-base arm64 5.36.0-6 [1726 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 zlib1g arm64 1:1.2.13.dfsg-1ubuntu3 [59.3 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 sysvinit-utils arm64 3.05-7ubuntu1 [25.8 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 systemd-sysv arm64 252.1-1ubuntu1 [11.4 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 debconf all 1.5.80 [125 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libssl3 arm64 3.0.5-2ubuntu2 [1752 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libkmod2 arm64 30+20220905-1ubuntu1 [47.7 kB] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libcap2 arm64 1:2.63-1 [27.4 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblz4-1 arm64 1.9.4-1 [63.4 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 systemd arm64 252.1-1ubuntu1 [2898 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsystemd-shared arm64 252.1-1ubuntu1 [1673 kB] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsystemd0 arm64 252.1-1ubuntu1 [321 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libcc1-0 arm64 12.2.0-10ubuntu1 [44.1 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libctf-nobfd0 arm64 2.39.50.20221211-0ubuntu1 [96.6 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgprofng0 arm64 2.39.50.20221211-0ubuntu1 [793 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libctf0 arm64 2.39.50.20221211-0ubuntu1 [93.0 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main arm64 libjansson4 arm64 2.14-2 [34.3 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.39.50.20221211-0ubuntu1 [3123 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libbinutils arm64 2.39.50.20221211-0ubuntu1 [762 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils-common arm64 2.39.50.20221211-0ubuntu1 [235 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils arm64 2.39.50.20221211-0ubuntu1 [3224 B] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgomp1 arm64 12.2.0-10ubuntu1 [122 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libitm1 arm64 12.2.0-10ubuntu1 [27.9 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libatomic1 arm64 12.2.0-10ubuntu1 [10.7 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libasan8 arm64 12.2.0-10ubuntu1 [2384 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblsan0 arm64 12.2.0-10ubuntu1 [1028 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libtsan2 arm64 12.2.0-10ubuntu1 [2514 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libubsan1 arm64 12.2.0-10ubuntu1 [957 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libhwasan0 arm64 12.2.0-10ubuntu1 [1109 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gcc-12-base arm64 12.2.0-10ubuntu1 [19.6 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libstdc++6 arm64 12.2.0-10ubuntu1 [647 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 g++-12 arm64 12.2.0-10ubuntu1 [10.9 MB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libstdc++-12-dev arm64 12.2.0-10ubuntu1 [2155 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgcc-12-dev arm64 12.2.0-10ubuntu1 [1157 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gcc-12 arm64 12.2.0-10ubuntu1 [19.1 MB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 cpp-12 arm64 12.2.0-10ubuntu1 [9581 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgcc-s1 arm64 12.2.0-10ubuntu1 [39.5 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libudev1 arm64 252.1-1ubuntu1 [86.7 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 adduser all 3.129ubuntu1 [59.0 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 openssl arm64 3.0.5-2ubuntu2 [1158 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main arm64 ca-certificates all 20211016ubuntu1 [141 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 dpkg-dev all 1.21.12ubuntu2 [1071 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libdpkg-perl all 1.21.12ubuntu2 [242 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 linux-libc-dev arm64 5.19.0-23.24 [1320 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.4 MB in 16s (5097 kB/s) (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu1_arm64.deb ... Unpacking coreutils (9.1-1ubuntu1) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu1) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.12ubuntu2_arm64.deb ... Unpacking dpkg (1.21.12ubuntu2) over (1.21.11ubuntu2) ... Setting up dpkg (1.21.12ubuntu2) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1_arm64.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) over (0.5.11+git20210903+057cd650a4ed-8ubuntu1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../perl_5.36.0-6_arm64.deb ... Unpacking perl (5.36.0-6) over (5.34.0-5ubuntu1) ... Selecting previously unselected package perl-modules-5.36. 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Setting up libhwasan0:arm64 (12.2.0-10ubuntu1) ... Setting up libasan8:arm64 (12.2.0-10ubuntu1) ... Setting up libtsan2:arm64 (12.2.0-10ubuntu1) ... Setting up libbinutils:arm64 (2.39.50.20221211-0ubuntu1) ... Setting up openssl (3.0.5-2ubuntu2) ... Setting up libcc1-0:arm64 (12.2.0-10ubuntu1) ... Setting up libperl5.36:arm64 (5.36.0-6) ... Setting up liblsan0:arm64 (12.2.0-10ubuntu1) ... Setting up libitm1:arm64 (12.2.0-10ubuntu1) ... Setting up libkmod2:arm64 (30+20220905-1ubuntu1) ... Setting up libctf0:arm64 (2.39.50.20221211-0ubuntu1) ... Setting up ca-certificates (20211016ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 0 added, 3 removed; done. Setting up perl (5.36.0-6) ... Setting up libgprofng0:arm64 (2.39.50.20221211-0ubuntu1) ... Setting up libgcc-12-dev:arm64 (12.2.0-10ubuntu1) ... Setting up libsystemd-shared:arm64 (252.1-1ubuntu1) ... Setting up libdpkg-perl (1.21.12ubuntu2) ... Setting up libstdc++-12-dev:arm64 (12.2.0-10ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.39.50.20221211-0ubuntu1) ... Setting up systemd (252.1-1ubuntu1) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.39.50.20221211-0ubuntu1) ... Setting up dpkg-dev (1.21.12ubuntu2) ... Setting up gcc-12 (12.2.0-10ubuntu1) ... Setting up g++-12 (12.2.0-10ubuntu1) ... Setting up systemd-sysv (252.1-1ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... (Reading database ... 15592 files and directories currently installed.) Purging configuration files for lsb-base (11.2ubuntu1) ... Processing triggers for ca-certificates (20211016ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24934573 arm64 lunar-proposed -c chroot:build-PACKAGEBUILD-24934573 --arch=arm64 --dist=lunar-proposed --nolog hmmer2_2.3.2+dfsg-8.dsc Initiating build PACKAGEBUILD-24934573 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-010.buildd +==============================================================================+ | hmmer2 2.3.2+dfsg-8 (arm64) Tue, 13 Dec 2022 11:38:58 +0000 | +==============================================================================+ Package: hmmer2 Version: 2.3.2+dfsg-8 Source Version: 2.3.2+dfsg-8 Distribution: lunar-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24934573/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/hmmer2-MAeD0W/resolver-ovovsK' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- hmmer2_2.3.2+dfsg-8.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/hmmer2-MAeD0W/hmmer2-2.3.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hmmer2-MAeD0W' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkg-config, dh-exec, rename, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkg-config, dh-exec, rename, 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 [413 B] Get:5 copy:/<>/apt_archive ./ Packages [494 B] Fetched 1864 B in 0s (114 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: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libperl4-corelibs-perl libpipeline1 libpkgconf3 libsquid-dev libsquid1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config pkgconf pkgconf-bin po-debconf rename Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff biosquid libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libperl4-corelibs-perl libpipeline1 libpkgconf3 libsquid-dev libsquid1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config pkgconf pkgconf-bin po-debconf rename sbuild-build-depends-main-dummy 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After this operation, 70.0 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [710 B] Get:2 http://ftpmaster.internal/ubuntu lunar/main arm64 libelf1 arm64 0.188-1 [51.2 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main arm64 libicu71 arm64 71.1-3ubuntu1 [10.5 MB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libxml2 arm64 2.9.14+dfsg-1.1 [722 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main arm64 bsdextrautils arm64 2.38.1-4ubuntu1 [69.1 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic-mgc arm64 1:5.41-4 [257 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic1 arm64 1:5.41-4 [85.0 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main arm64 file arm64 1:5.41-4 [21.6 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext-base arm64 0.21-10 [36.5 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main arm64 libuchardet0 arm64 0.0.7-1build2 [77.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main arm64 groff-base arm64 1.22.4-9 [899 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main arm64 libpipeline1 arm64 1.5.7-1 [23.3 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main arm64 man-db arm64 2.11.1-1 [1213 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main arm64 m4 arm64 1.4.19-1 [240 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main arm64 autoconf all 2.71-2 [338 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main arm64 autopoint all 0.21-10 [421 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main arm64 libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main arm64 libtool all 2.4.7-5 [166 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-autoreconf all 20 [16.1 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main arm64 libsub-override-perl all 0.09-4 [8706 B] Get:24 http://ftpmaster.internal/ubuntu lunar/main arm64 libfile-stripnondeterminism-perl all 1.13.0-2 [18.2 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-strip-nondeterminism all 1.13.0-2 [5308 B] Get:26 http://ftpmaster.internal/ubuntu lunar/main arm64 libdw1 arm64 0.188-1 [245 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main arm64 dwz arm64 0.14+20220924-2 [110 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext arm64 0.21-10 [842 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main arm64 debhelper all 13.10.1ubuntu1 [924 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main arm64 libperl4-corelibs-perl all 0.004-3 [37.9 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/universe arm64 libpkgconf3 arm64 1.8.0-11 [29.4 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/universe arm64 libsquid1 arm64 1.9g+cvs20050121-12 [70.7 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/universe arm64 libsquid-dev arm64 1.9g+cvs20050121-12 [139 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/universe arm64 pkgconf-bin arm64 1.8.0-11 [20.4 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/universe arm64 pkgconf arm64 1.8.0-11 [16.4 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 pkg-config arm64 1.8.0-11 [5414 B] Get:40 http://ftpmaster.internal/ubuntu lunar/universe arm64 rename all 1.31-1 [20.1 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-exec arm64 0.27 [25.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.7 MB in 3s (6430 kB/s) Selecting previously unselected package libelf1:arm64. (Reading database ... 15592 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.188-1_arm64.deb ... Unpacking libelf1:arm64 (0.188-1) ... Selecting previously unselected package libicu71:arm64. Preparing to unpack .../01-libicu71_71.1-3ubuntu1_arm64.deb ... Unpacking libicu71:arm64 (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.1_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../03-bsdextrautils_2.38.1-4ubuntu1_arm64.deb ... Unpacking bsdextrautils (2.38.1-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.41-4_arm64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../05-libmagic1_1%3a5.41-4_arm64.deb ... Unpacking libmagic1:arm64 (1:5.41-4) ... 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Setting up libmagic1:arm64 (1:5.41-4) ... Setting up gettext-base (0.21-10) ... Setting up m4 (1.4.19-1) ... Setting up rename (1.31-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.41-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.0-11) ... Setting up autopoint (0.21-10) ... Setting up pkgconf-bin (1.8.0-11) ... Setting up autoconf (2.71-2) ... Setting up libsquid1 (1.9g+cvs20050121-12) ... Setting up libuchardet0:arm64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1) ... 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 (1.13.0-2) ... Setting up libdw1:arm64 (0.188-1) ... Setting up gettext (0.21-10) ... Setting up libtool (2.4.7-5) ... Setting up libsquid-dev (1.9g+cvs20050121-12) ... Setting up pkgconf:arm64 (1.8.0-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.0-11) ... Setting up dh-strip-nondeterminism (1.13.0-2) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up debugedit (1:5.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.1-1) ... 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 (13.10.1ubuntu1) ... Setting up dh-exec (0.27) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 arm64 (aarch64) Toolchain package versions: binutils_2.39.50.20221211-0ubuntu1 dpkg-dev_1.21.12ubuntu2 g++-12_12.2.0-10ubuntu1 gcc-12_12.2.0-10ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-10ubuntu1 libstdc++6_12.2.0-10ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39.50.20221211-0ubuntu1 binutils-aarch64-linux-gnu_2.39.50.20221211-0ubuntu1 binutils-common_2.39.50.20221211-0ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_9.1-1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-10ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.80 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-exec_0.27 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dpkg_1.21.12ubuntu2 dpkg-dev_1.21.12ubuntu2 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-10ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-10ubuntu1 gcc-12-base_12.2.0-10ubuntu1 gettext_0.21-10 gettext-base_0.21-10 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-2 libapparmor1_3.0.7-1ubuntu4 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-10ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-10ubuntu1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1ubuntu2 libaudit1_1:3.0.7-1ubuntu2 libbinutils_2.39.50.20221211-0ubuntu1 libblkid1_2.38.1-4ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcap-ng0_0.8.3-1build1 libcap2_1:2.63-1 libcc1-0_12.2.0-10ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.39.50.20221211-0ubuntu1 libctf0_2.39.50.20221211-0ubuntu1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.12ubuntu2 libdw1_0.188-1 libelf1_0.188-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfakeroot_1.30.1-1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libgcc-12-dev_12.2.0-10ubuntu1 libgcc-s1_12.2.0-10ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.7-2ubuntu2 libgomp1_12.2.0-10ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.39.50.20221211-0ubuntu1 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhwasan0_12.2.0-10ubuntu1 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_12.2.0-10ubuntu1 libjansson4_2.14-2 libjson-c5_0.16-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkmod2_30+20220905-1ubuntu1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.2.0-10ubuntu1 liblz4-1_1.9.4-1 liblzma5_5.2.9-0.0 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.2.1-2build1 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libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_12.2.0-10ubuntu1 libubsan1_12.2.0-10ubuntu1 libuchardet0_0.0.7-1build2 libudev1_252.1-1ubuntu1 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.0-23.24 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.46.6~rc1-1ubuntu1 lto-disabled-list_36 m4_1.4.19-1 make_4.3-4.1build1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-2ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.34_5.34.0-5ubuntu1 perl-modules-5.36_5.36.0-6 pinentry-curses_1.2.1-1ubuntu1 pkg-config_1.8.0-11 pkgbinarymangler_149 pkgconf_1.8.0-11 pkgconf-bin_1.8.0-11 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 readline-common_8.2-1.2 rename_1.31-1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_252.1-1ubuntu1 systemd-sysv_252.1-1ubuntu1 sysvinit-utils_3.05-7ubuntu1 tar_1.34+dfsg-1.1 tzdata_2022g-0ubuntu2 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 xz-utils_5.2.9-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: hmmer2 Binary: hmmer2, hmmer2-doc, libhmmer2-dev Architecture: any all Version: 2.3.2+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Laszlo Kajan Homepage: http://hmmer.janelia.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/hmmer2 Vcs-Git: https://salsa.debian.org/med-team/hmmer2.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, libperl4-corelibs-perl, libsquid-dev, pkg-config Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkg-config, dh-exec, rename Package-List: hmmer2 deb science optional arch=any hmmer2-doc deb doc optional arch=all libhmmer2-dev deb libdevel optional arch=any Checksums-Sha1: 7467176def6174e90edd239558b6fcc2cb8033df 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 6d6d658fa934eb53c22780e16c7899171587dbcc 19968 hmmer2_2.3.2+dfsg-8.debian.tar.xz Checksums-Sha256: f9cd50acc23743648cb7de020c249bce396c3d07e0afe7e5418620cffa07bb44 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 9cfce31a7ad72d780abfd68ddef533c87ae4388dc9e9e7e9680630f25791ad0d 19968 hmmer2_2.3.2+dfsg-8.debian.tar.xz Files: 4f8c9fd7c7de00fb8cfab499931ee4ba 331828 hmmer2_2.3.2+dfsg.orig.tar.xz a223d42d33db0c92ee26caccbc9a706b 19968 hmmer2_2.3.2+dfsg-8.debian.tar.xz 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gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting hmmer2 in /<> dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch dpkg-source: info: applying add-runstatedir-option.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-24934573 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24934573 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24934573 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 hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' if [ -e configure_not_used ] ; then mv configure_not_used configure; fi rm -f configure.ac make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' cp -a debian/missing-sources/configure.ac . mv configure configure_not_used dh_autoreconf configure.ac:111: warning: underquoted definition of CHECK_GNU_MAKE configure.ac:111: run info Automake 'Extending aclocal' configure.ac:111: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:153: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.ac:153: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.ac:153: the top level configure.ac:479: warning: The macro `AC_LANG_C' is obsolete. configure.ac:479: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:281: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:479: the top level configure.ac:479: warning: The macro `AC_TRY_LINK' is obsolete. configure.ac:479: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... configure.ac:281: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:479: the top level make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... yes checking for pthread_attr_setscope... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/src' gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmalign.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c alphabet.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c core_algorithms.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c debug.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c display.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c emit.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c emulation.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c histogram.c histogram.c: In function ‘ExtremeValueSetHistogram’: histogram.c:725:23: warning: implicit declaration of function ‘IncompleteGamma’ [-Wimplicit-function-declaration] 725 | h->chip = (float) IncompleteGamma((double)(nbins-1-ndegrees)/2., | ^~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmio.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c mathsupport.c mathsupport.c: In function ‘Logp_cvec’: mathsupport.c:229:15: warning: implicit declaration of function ‘Gammln’ [-Wimplicit-function-declaration] 229 | lnp += Gammln(alpha[x] + cvec[x]); | ^~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c masks.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c misc.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c modelmakers.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c plan7.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c plan9.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c postprob.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c prior.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c pvm.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c threads.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c tophits.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c trace.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmconvert.c hmmcalibrate.c: In function ‘workpool_start’: hmmcalibrate.c:646:3: warning: implicit declaration of function ‘pthread_setconcurrency’ [-Wimplicit-function-declaration] 646 | pthread_setconcurrency(num_threads+1); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmemit.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmpfam.c hmmpfam.c: In function ‘workpool_start’: hmmpfam.c:1032:3: warning: implicit declaration of function ‘pthread_setconcurrency’ [-Wimplicit-function-declaration] 1032 | pthread_setconcurrency(num_threads+1); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmsearch.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm hmmsearch.c: In function ‘workpool_start’: hmmsearch.c:1021:3: warning: implicit declaration of function ‘pthread_setconcurrency’ [-Wimplicit-function-declaration] 1021 | pthread_setconcurrency(num_threads+1); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DHAVE_CONFIG_H -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/testsuite' gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/<>=. -fdebug-prefix-map=/<>=/usr/src/hmmer2-2.3.2+dfsg-8 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/<>/testsuite' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/<>' (cd testsuite; make check) make[3]: Entering directory '/<>/testsuite' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Tue Dec 13 11:39:24 UTC 2022 Linux bos01-arm64-010 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux make[3]: Leaving directory '/<>/testsuite' make[2]: Leaving directory '/<>' rm -f testsuite/*.ssi cd testsuite && make clean make[2]: Entering directory '/<>/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/<>/testsuite' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- prefix=/<>/debian/tmp make -j4 install DESTDIR=/<>/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/<>/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/<>' mkdir -p /<>/debian/tmp/bin mkdir -p /<>/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /<>/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /<>/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/<>' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /<>/debian/tmp/bin/* cd /<>/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /<>/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /<>/debian/tmp/share/man/man1/hmm2er.1 /<>/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /<>/debian/tmp/share/man/man1/* make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs -k NOTES make[1]: Leaving directory '/<>' debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples mkdir -p /<>/debian/hmmer2/usr/share/doc/hmmer2/examples; sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc cp -a testsuite/* /<>/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /<>/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /<>/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#../tut#./tut#g" /<>/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /<>/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/<>^.^g" make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/hmmer2/usr/bin/hmm2search: Unknown DWARF DW_FORM_0x1f20 3696a4c0f98b5c137af0e24b0870708b1259aad8 debugedit: debian/hmmer2/usr/bin/hmm2emit: Unknown DWARF DW_FORM_0x1f20 07e2d838b0fdc921177a9e5b7d25ee72eb4e4845 debugedit: debian/hmmer2/usr/bin/hmm2fetch: Unknown DWARF DW_FORM_0x1f20 31e11f00d16a59c3c140f40bf01e803bda2771a3 debugedit: debian/hmmer2/usr/bin/hmm2build: Unknown DWARF DW_FORM_0x1f20 2eb7f434f8faa0eb61e10499e2a4f55622d052bf debugedit: debian/hmmer2/usr/bin/hmm2index: Unknown DWARF DW_FORM_0x1f20 d75dcbd0dfc7c4ecd4b0f6f881416e0dac9ff5f4 debugedit: debian/hmmer2/usr/bin/hmm2convert: Unknown DWARF DW_FORM_0x1f20 0a3f52961d188dd06dd856a7d76d63089df20b15 debugedit: debian/hmmer2/usr/bin/hmm2calibrate: Unknown DWARF DW_FORM_0x1f20 f533af7121189f739dee53e836e978c038d78340 debugedit: debian/hmmer2/usr/bin/hmm2pfam: Unknown DWARF DW_FORM_0x1f20 f478bceddf5e028e11f045356418e47d7a63b601 debugedit: debian/hmmer2/usr/bin/hmm2align: Unknown DWARF DW_FORM_0x1f20 5be15fc0e0fc8abd3205f8abc1f52117e7549d9d dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libhmmer2-dev (in debian/libhmmer2-dev); do_strip: , oemstrip: pkgstriptranslations: processing hmmer2 (in debian/hmmer2); do_strip: , oemstrip: pkgstriptranslations: processing hmmer2-dbgsym (in debian/.debhelper/hmmer2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libhmmer2-dev/DEBIAN/control, package libhmmer2-dev, directory debian/libhmmer2-dev .. removing usr/share/doc/libhmmer2-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhmmer2-dev) ... pkgstripfiles: processing control file: debian/hmmer2/DEBIAN/control, package hmmer2, directory debian/hmmer2 .. removing usr/share/doc/hmmer2/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package hmmer2 ... pkgstripfiles: processing control file: debian/.debhelper/hmmer2/dbgsym-root/DEBIAN/control, package hmmer2-dbgsym, directory debian/.debhelper/hmmer2/dbgsym-root pkgstripfiles: No PNG files. dpkg-deb: building package 'hmmer2-dbgsym' in 'debian/.debhelper/scratch-space/build-hmmer2/hmmer2-dbgsym_2.3.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-8_arm64.deb'. Renaming hmmer2-dbgsym_2.3.2+dfsg-8_arm64.deb to hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhmmer2-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=any -O../hmmer2_2.3.2+dfsg-8_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../hmmer2_2.3.2+dfsg-8_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-13T11:39:30Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ hmmer2_2.3.2+dfsg-8_arm64.changes: ---------------------------------- Format: 1.8 Date: Sun, 11 Dec 2022 16:58:23 +0100 Source: hmmer2 Binary: hmmer2 libhmmer2-dev Built-For-Profiles: noudeb Architecture: arm64 Version: 2.3.2+dfsg-8 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: hmmer2 - profile hidden Markov models for protein sequence analysis libhmmer2-dev - profile hidden Markov models for protein sequence analysis (devel Closes: 1025739 Changes: hmmer2 (2.3.2+dfsg-8) unstable; urgency=medium . * Provide configure.ac as source for configure Closes: #1025739 * Fix watchfile to detect new versions on github * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 2f9497899dbd0639daca2375c6654c22f415d2c6 554554 hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb 6f46e500a11103ec78bd9d0861c983179c7566e5 6285 hmmer2_2.3.2+dfsg-8_arm64.buildinfo fbcbb3842fbb9a85c963ab0124e7b1e55d22baab 307634 hmmer2_2.3.2+dfsg-8_arm64.deb a4c939a005725fd93ccfc1ba884d23e33d5a2b7b 99570 libhmmer2-dev_2.3.2+dfsg-8_arm64.deb Checksums-Sha256: a5ccdb427b6f286b9c8d8758394896a911cc1bba103dd0e95804fcf6fe882554 554554 hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb f6bda66e620cb4973a2280458834c69dcdd54e7f97797c5803ef1b96693432dd 6285 hmmer2_2.3.2+dfsg-8_arm64.buildinfo 0af1ed7b7fa71f28c48fb76f87c361d4b34a53f459418009ebc31b468263dd55 307634 hmmer2_2.3.2+dfsg-8_arm64.deb e6104e56af63ec8e52502793cc7587dd6efae966eba208d0a60b1b696d650d13 99570 libhmmer2-dev_2.3.2+dfsg-8_arm64.deb Files: 617168ca6956c56174776fd5a1bcf5fd 554554 debug optional hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb 2af601bf59370539b63f752e48e3f0af 6285 science optional hmmer2_2.3.2+dfsg-8_arm64.buildinfo eaf917b6f49265dbbf51a88153c5efbc 307634 science optional hmmer2_2.3.2+dfsg-8_arm64.deb 7c6072b1d85d6f62580fa2ad331aa2d3 99570 libdevel optional libhmmer2-dev_2.3.2+dfsg-8_arm64.deb /<>/hmmer2_2.3.2+dfsg-8_arm64.changes.new could not be renamed to /<>/hmmer2_2.3.2+dfsg-8_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym libhmmer2-dev Architecture: arm64 Version: 2.3.2+dfsg-8 Checksums-Md5: 617168ca6956c56174776fd5a1bcf5fd 554554 hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb eaf917b6f49265dbbf51a88153c5efbc 307634 hmmer2_2.3.2+dfsg-8_arm64.deb 7c6072b1d85d6f62580fa2ad331aa2d3 99570 libhmmer2-dev_2.3.2+dfsg-8_arm64.deb Checksums-Sha1: 2f9497899dbd0639daca2375c6654c22f415d2c6 554554 hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb fbcbb3842fbb9a85c963ab0124e7b1e55d22baab 307634 hmmer2_2.3.2+dfsg-8_arm64.deb a4c939a005725fd93ccfc1ba884d23e33d5a2b7b 99570 libhmmer2-dev_2.3.2+dfsg-8_arm64.deb Checksums-Sha256: a5ccdb427b6f286b9c8d8758394896a911cc1bba103dd0e95804fcf6fe882554 554554 hmmer2-dbgsym_2.3.2+dfsg-8_arm64.ddeb 0af1ed7b7fa71f28c48fb76f87c361d4b34a53f459418009ebc31b468263dd55 307634 hmmer2_2.3.2+dfsg-8_arm64.deb e6104e56af63ec8e52502793cc7587dd6efae966eba208d0a60b1b696d650d13 99570 libhmmer2-dev_2.3.2+dfsg-8_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Tue, 13 Dec 2022 11:39:30 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39.50.20221211-0ubuntu1), binutils-aarch64-linux-gnu (= 2.39.50.20221211-0ubuntu1), binutils-common (= 2.39.50.20221211-0ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-10ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.80), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-exec (= 0.27), dh-strip-nondeterminism (= 1.13.0-2), diffutils (= 1:3.8-1), dpkg (= 1.21.12ubuntu2), dpkg-dev (= 1.21.12ubuntu2), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-10ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-10ubuntu1), gcc-12-base (= 12.2.0-10ubuntu1), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-10ubuntu1), libatomic1 (= 12.2.0-10ubuntu1), libattr1 (= 1:2.5.1-3), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libbinutils (= 2.39.50.20221211-0ubuntu1), libblkid1 (= 2.38.1-4ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.63-1), libcc1-0 (= 12.2.0-10ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39.50.20221211-0ubuntu1), libctf0 (= 2.39.50.20221211-0ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdpkg-perl (= 1.21.12ubuntu2), libdw1 (= 0.188-1), libelf1 (= 0.188-1), libfile-stripnondeterminism-perl (= 1.13.0-2), libgcc-12-dev (= 12.2.0-10ubuntu1), libgcc-s1 (= 12.2.0-10ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgomp1 (= 12.2.0-10ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39.50.20221211-0ubuntu1), libgssapi-krb5-2 (= 1.20.1-1), libhwasan0 (= 12.2.0-10ubuntu1), libicu71 (= 71.1-3ubuntu1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-10ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20.1-1), libkrb5support0 (= 1.20.1-1), liblsan0 (= 12.2.0-10ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.2.9-0.0), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.40-1ubuntu1), libperl4-corelibs-perl (= 0.004-3), libperl5.36 (= 5.36.0-6), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.0-11), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build1), libsmartcols1 (= 2.38.1-4ubuntu1), libsquid-dev (= 1.9g+cvs20050121-12), libsquid1 (= 1.9g+cvs20050121-12), libssl3 (= 3.0.5-2ubuntu2), libstdc++-12-dev (= 12.2.0-10ubuntu1), libstdc++6 (= 12.2.0-10ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.1-1ubuntu1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-10ubuntu1), libubsan1 (= 12.2.0-10ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.1-1ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 36), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.36.0-6), perl-base (= 5.36.0-6), perl-modules-5.36 (= 5.36.0-6), pkg-config (= 1.8.0-11), pkgconf (= 1.8.0-11), pkgconf-bin (= 1.8.0-11), po-debconf (= 1.0.21+nmu1), rename (= 1.31-1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.05-7ubuntu1), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), xz-utils (= 5.2.9-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu3) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1670774303" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ hmmer2_2.3.2+dfsg-8_arm64.deb ----------------------------- new Debian package, version 2.0. size 307634 bytes: control archive=2528 bytes. 922 bytes, 21 lines control 5093 bytes, 69 lines md5sums Package: hmmer2 Version: 2.3.2+dfsg-8 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1426 Depends: libc6 (>= 2.34), libsquid1 (>= 1.9g+cvs20050121) Recommends: biosquid Suggests: hmmer2-doc (>= 2.3.2+dfsg-8) Section: science Priority: optional Homepage: http://hmmer.janelia.org/ Description: profile hidden Markov models for protein sequence analysis HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. drwxr-xr-x root/root 0 2022-12-11 15:58 ./ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/bin/ -rwxr-xr-x root/root 134080 2022-12-11 15:58 ./usr/bin/hmm2align -rwxr-xr-x root/root 70656 2022-12-11 15:58 ./usr/bin/hmm2build -rwxr-xr-x root/root 68472 2022-12-11 15:58 ./usr/bin/hmm2calibrate -rwxr-xr-x root/root 68328 2022-12-11 15:58 ./usr/bin/hmm2convert -rwxr-xr-x root/root 68248 2022-12-11 15:58 ./usr/bin/hmm2emit -rwxr-xr-x root/root 67960 2022-12-11 15:58 ./usr/bin/hmm2fetch -rwxr-xr-x root/root 67872 2022-12-11 15:58 ./usr/bin/hmm2index -rwxr-xr-x root/root 134896 2022-12-11 15:58 ./usr/bin/hmm2pfam -rwxr-xr-x root/root 134688 2022-12-11 15:58 ./usr/bin/hmm2search drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/lib/hmmer2/ lrwxrwxrwx root/root 0 2022-12-11 15:58 ./usr/lib/hmmer2/hmmindex -> ../../bin/hmm2index lrwxrwxrwx root/root 0 2022-12-11 15:58 ./usr/lib/hmmer2/hmmpfam -> ../../bin/hmm2pfam drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/doc/hmmer2/ -rw-r--r-- root/root 2293 2022-12-11 15:58 ./usr/share/doc/hmmer2/00README -rw-r--r-- root/root 344 2022-12-11 15:58 ./usr/share/doc/hmmer2/NEWS.Debian.gz lrwxrwxrwx root/root 0 2022-12-11 15:58 ./usr/share/doc/hmmer2/NOTES.gz -> changelog.gz -rw-r--r-- root/root 615 2022-12-11 15:58 ./usr/share/doc/hmmer2/README.Debian -rw-r--r-- root/root 578 2022-12-11 15:58 ./usr/share/doc/hmmer2/changelog.Debian.gz -rw-r--r-- root/root 1411 2022-12-11 15:58 ./usr/share/doc/hmmer2/copyright drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/doc/hmmer2/examples/ -rw-r--r-- root/root 1972 2022-12-11 15:58 ./usr/share/doc/hmmer2/examples/Makefile -rw-r--r-- root/root 1725 2022-12-11 15:58 ./usr/share/doc/hmmer2/examples/Makefile.in -rw-r--r-- root/root 392 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.fa -rw-r--r-- root/root 126 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.nfa -rw-r--r-- root/root 168 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.nslx -rw-r--r-- root/root 2122 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.pam -rw-r--r-- root/root 2816 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.pri -rw-r--r-- root/root 297 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.slx -rw-r--r-- root/root 3271 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/Optiontests.sto -rw-r--r-- root/root 2684 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/README -rw-r--r-- root/root 7729 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/alignalign_test.c -rw-r--r-- root/root 9913 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./usr/share/doc/hmmer2/examples/weeviterbi_test.c -rw-r--r-- root/root 27073 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/weeviterbi_test.hmm -rw-r--r-- root/root 535 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/weeviterbi_test.seq drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/man/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/man/man1/ -rw-r--r-- root/root 1748 2022-12-11 15:58 ./usr/share/man/man1/hmm2align.1.gz -rw-r--r-- root/root 4765 2022-12-11 15:58 ./usr/share/man/man1/hmm2build.1.gz -rw-r--r-- root/root 1703 2022-12-11 15:58 ./usr/share/man/man1/hmm2calibrate.1.gz -rw-r--r-- root/root 1113 2022-12-11 15:58 ./usr/share/man/man1/hmm2convert.1.gz -rw-r--r-- root/root 1364 2022-12-11 15:58 ./usr/share/man/man1/hmm2emit.1.gz -rw-r--r-- root/root 945 2022-12-11 15:58 ./usr/share/man/man1/hmm2fetch.1.gz -rw-r--r-- root/root 752 2022-12-11 15:58 ./usr/share/man/man1/hmm2index.1.gz -rw-r--r-- root/root 3395 2022-12-11 15:58 ./usr/share/man/man1/hmm2pfam.1.gz -rw-r--r-- root/root 3046 2022-12-11 15:58 ./usr/share/man/man1/hmm2search.1.gz -rw-r--r-- root/root 1691 2022-12-11 15:58 ./usr/share/man/man1/hmmer2.1.gz libhmmer2-dev_2.3.2+dfsg-8_arm64.deb ------------------------------------ new Debian package, version 2.0. size 99570 bytes: control archive=1001 bytes. 953 bytes, 23 lines control 621 bytes, 9 lines md5sums Package: libhmmer2-dev Source: hmmer2 Version: 2.3.2+dfsg-8 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 324 Section: libdevel Priority: optional Multi-Arch: same Homepage: http://hmmer.janelia.org/ Description: profile hidden Markov models for protein sequence analysis (devel) HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. . This package contains header files and static library that can be used to link against libhmmer. drwxr-xr-x root/root 0 2022-12-11 15:58 ./ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/include/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/include/hmmer2/ -rw-r--r-- root/root 4524 2022-12-11 15:58 ./usr/include/hmmer2/config.h -rw-r--r-- root/root 16093 2022-12-11 15:58 ./usr/include/hmmer2/funcs.h -rw-r--r-- root/root 1201 2003-10-04 19:01 ./usr/include/hmmer2/globals.h -rw-r--r-- root/root 1733 2003-10-04 19:01 ./usr/include/hmmer2/postprob.h -rw-r--r-- root/root 24821 2003-10-04 19:01 ./usr/include/hmmer2/structs.h drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/lib/aarch64-linux-gnu/ -rw-r--r-- root/root 260568 2022-12-11 15:58 ./usr/lib/aarch64-linux-gnu/libhmmer.a drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/lib/aarch64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 262 2022-12-11 15:58 ./usr/lib/aarch64-linux-gnu/pkgconfig/libhmmer2.pc drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-11 15:58 ./usr/share/doc/libhmmer2-dev/ lrwxrwxrwx root/root 0 2022-12-11 15:58 ./usr/share/doc/libhmmer2-dev/NOTES.gz -> changelog.gz -rw-r--r-- root/root 582 2022-12-11 15:58 ./usr/share/doc/libhmmer2-dev/changelog.Debian.gz -rw-r--r-- root/root 1411 2022-12-11 15:58 ./usr/share/doc/libhmmer2-dev/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 18232 Build-Time: 23 Distribution: lunar-proposed Host Architecture: arm64 Install-Time: 8 Job: hmmer2_2.3.2+dfsg-8.dsc Machine Architecture: arm64 Package: hmmer2 Package-Time: 32 Source-Version: 2.3.2+dfsg-8 Space: 18232 Status: successful Version: 2.3.2+dfsg-8 -------------------------------------------------------------------------------- Finished at 2022-12-13T11:39:30Z Build needed 00:00:32, 18232k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-24934573 Scanning for processes to kill in build PACKAGEBUILD-24934573