sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | hmmer2 2.3.2+dfsg-12 (arm64) Mon, 14 Oct 2024 21:04:01 +0000 | +==============================================================================+ Package: hmmer2 Version: 2.3.2+dfsg-12 Source Version: 2.3.2+dfsg-12 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-919bdb1e-8968-4cb5-81a2-143fdd0d9473' with '<>' I: NOTICE: Log filtering will replace 'build/hmmer2-l8A5h3/resolver-CYG3hj' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [202 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-10-14-2004.38-F-2024-10-14-0204.32.pdiff [46.4 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-10-14-2004.38-F-2024-10-14-0204.32.pdiff [54.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-10-14-2004.38-F-2024-10-14-0204.32.pdiff [46.4 kB] Get:6 http://localhost:3142/debian sid/main arm64 Packages [9915 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-10-14-2004.38-F-2024-10-14-0204.32.pdiff [54.6 kB] Fetched 10.3 MB in 3s (3687 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: libperl5.38t64 perl-modules-5.38 Use 'apt autoremove' to remove them. The following NEW packages will be installed: libperl5.40 perl-modules-5.40 The following packages will be upgraded: perl perl-base 2 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 9290 kB of archives. After this operation, 50.7 MB of additional disk space will be used. Get:1 http://localhost:3142/debian sid/main amd64 perl-modules-5.40 all 5.40.0-6 [3022 kB] Get:2 http://localhost:3142/debian sid/main amd64 libperl5.40 amd64 5.40.0-6 [4326 kB] Get:3 http://localhost:3142/debian sid/main amd64 perl amd64 5.40.0-6 [267 kB] Get:4 http://localhost:3142/debian sid/main amd64 perl-base amd64 5.40.0-6 [1675 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9290 kB in 0s (176 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12823 files and directories currently installed.) Preparing to unpack .../perl_5.40.0-6_amd64.deb ... Unpacking perl (5.40.0-6) over (5.38.2-5) ... Selecting previously unselected package perl-modules-5.40. Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... Unpacking perl-modules-5.40 (5.40.0-6) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../libperl5.40_5.40.0-6_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-6) ... Preparing to unpack .../perl-base_5.40.0-6_amd64.deb ... Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... Setting up perl-base (5.40.0-6) ... Setting up perl-modules-5.40 (5.40.0-6) ... Setting up libperl5.40:amd64 (5.40.0-6) ... Setting up perl (5.40.0-6) ... Processing triggers for libc-bin (2.40-3) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 355 kB of source archives. Get:1 http://localhost:3142/debian sid/main hmmer2 2.3.2+dfsg-12 (dsc) [2236 B] Get:2 http://localhost:3142/debian sid/main hmmer2 2.3.2+dfsg-12 (tar) [332 kB] Get:3 http://localhost:3142/debian sid/main hmmer2 2.3.2+dfsg-12 (diff) [21.1 kB] Fetched 355 kB in 1s (580 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hmmer2-l8A5h3/hmmer2-2.3.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hmmer2-l8A5h3' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [778 B] Get:5 copy:/<>/apt_archive ./ Packages [821 B] Fetched 2208 B in 0s (0 B/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... Execute external solver... The following packages were automatically installed and are no longer required: libperl5.38t64 login mount perl-modules-5.38 tzdata Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libperl4-corelibs-perl libpipeline1 libpkgconf3 libsquid-dev:arm64 libsquid1t64:arm64 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml2 linux-libc-dev-arm64-cross m4 man-db pkgconf:arm64 pkgconf-bin po-debconf rename sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales cpp-14-doc cpp-doc dh-make gcc-14-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 biosquid:arm64 libstdc++-14-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libperl4-corelibs-perl libpipeline1 libpkgconf3 libsquid-dev:arm64 libsquid1t64:arm64 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml2 linux-libc-dev-arm64-cross m4 man-db pkgconf:arm64 pkgconf-bin po-debconf rename sbuild-build-depends-main-dummy:arm64 sensible-utils 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 99.5 MB of archives. After this operation, 442 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [956 B] Get:2 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get:10 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://localhost:3142/debian sid/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://localhost:3142/debian sid/main amd64 autoconf all 2.72-3 [493 kB] Get:14 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://localhost:3142/debian sid/main amd64 autopoint all 0.22.5-2 [723 kB] Get:17 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.43.1-5 [3543 kB] Get:18 http://localhost:3142/debian sid/main amd64 gcc-14-aarch64-linux-gnu-base amd64 14.2.0-6cross1 [47.0 kB] Get:19 http://localhost:3142/debian sid/main amd64 cpp-14-aarch64-linux-gnu amd64 14.2.0-6cross1 [11.2 MB] Get:20 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:14.2.0-1 [4844 B] Get:21 http://localhost:3142/debian sid/main amd64 gcc-14-cross-base all 14.2.0-6cross1 [42.2 kB] Get:22 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.40-3cross1 [1141 kB] Get:23 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 14.2.0-6cross1 [54.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 14.2.0-6cross1 [91.7 kB] Get:25 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 14.2.0-6cross1 [25.9 kB] Get:26 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 14.2.0-6cross1 [10.3 kB] Get:27 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 14.2.0-6cross1 [436 kB] Get:28 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 14.2.0-6cross1 [201 kB] Get:29 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 14.2.0-6cross1 [415 kB] Get:30 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 14.2.0-6cross1 [546 kB] Get:31 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 14.2.0-6cross1 [186 kB] Get:32 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 14.2.0-6cross1 [256 kB] Get:33 http://localhost:3142/debian sid/main amd64 libgcc-14-dev-arm64-cross all 14.2.0-6cross1 [2458 kB] Get:34 http://localhost:3142/debian sid/main amd64 gcc-14-aarch64-linux-gnu amd64 14.2.0-6cross1 [21.6 MB] Get:35 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:14.2.0-1 [1448 B] Get:36 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.11.2-1cross1 [2241 kB] Get:37 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.40-3cross1 [1585 kB] Get:38 http://localhost:3142/debian sid/main amd64 libstdc++-14-dev-arm64-cross all 14.2.0-6cross1 [2543 kB] Get:39 http://localhost:3142/debian sid/main amd64 g++-14-aarch64-linux-gnu amd64 14.2.0-6cross1 [12.2 MB] Get:40 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:14.2.0-1 [1200 B] Get:41 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.12 [3548 B] Get:42 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:43 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:44 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:45 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:46 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:47 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:48 http://localhost:3142/debian sid/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:49 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:50 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:51 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:52 http://localhost:3142/debian sid/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:53 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:54 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:55 http://localhost:3142/debian sid/main amd64 debhelper all 13.20 [915 kB] Get:56 http://localhost:3142/debian sid/main amd64 dh-exec amd64 0.30 [25.6 kB] Get:57 http://localhost:3142/debian sid/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:58 http://localhost:3142/debian sid/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:59 http://localhost:3142/debian sid/main arm64 gcc-14-base arm64 14.2.0-6 [46.8 kB] Get:60 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 14.2.0-6 [54.0 kB] Get:61 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.40-3 [2453 kB] Get:62 http://localhost:3142/debian sid/main arm64 libasan8 arm64 14.2.0-6 [2578 kB] Get:63 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 14.2.0-6 [10.1 kB] Get:64 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.36-5 [91.6 kB] Get:65 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB] Get:66 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB] Get:67 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 14.2.0-6 [124 kB] Get:68 http://localhost:3142/debian sid/main arm64 libitm1 arm64 14.2.0-6 [24.1 kB] Get:69 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 14.2.0-6 [1162 kB] Get:70 http://localhost:3142/debian sid/main arm64 libtsan2 arm64 14.2.0-6 [2386 kB] Get:71 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 14.2.0-6 [637 kB] Get:72 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 14.2.0-6 [1039 kB] Get:73 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 14.2.0-6 [1442 kB] Get:74 http://localhost:3142/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-6 [2364 kB] Get:75 http://localhost:3142/debian sid/main amd64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] Get:76 http://localhost:3142/debian sid/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:77 http://localhost:3142/debian sid/main arm64 libsquid1t64 arm64 1.9g+cvs20050121-15.1 [71.0 kB] Get:78 http://localhost:3142/debian sid/main arm64 libsquid-dev arm64 1.9g+cvs20050121-15.1 [140 kB] Get:79 http://localhost:3142/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-6 [2265 kB] Get:80 http://localhost:3142/debian sid/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:81 http://localhost:3142/debian sid/main arm64 pkgconf arm64 1.8.1-3 [26.0 kB] Get:82 http://localhost:3142/debian sid/main amd64 rename all 2.02-1 [21.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 99.5 MB in 1s (198 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14904 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblsan0-arm64-cross (14.2.0-6cross1) ... Setting up libgomp1-arm64-cross (14.2.0-6cross1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libhwasan0-arm64-cross (14.2.0-6cross1) ... Setting up libc6-dev-arm64-cross (2.40-3cross1) ... Setting up pkgconf:arm64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (14.2.0-6cross1) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up cpp-14-aarch64-linux-gnu (14.2.0-6cross1) ... Setting up groff-base (1.23.0-5) ... Setting up libasan8-arm64-cross (14.2.0-6cross1) ... Setting up libtsan2-arm64-cross (14.2.0-6cross1) ... Setting up libubsan1-arm64-cross (14.2.0-6cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cpp-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libgcc-14-dev-arm64-cross (14.2.0-6cross1) ... Setting up libstdc++-14-dev-arm64-cross (14.2.0-6cross1) ... Setting up gcc-14-aarch64-linux-gnu (14.2.0-6cross1) ... Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ... Setting up g++-14-aarch64-linux-gnu (14.2.0-6cross1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ... Setting up crossbuild-essential-arm64 (12.12) ... Setting up libgcc-s1:arm64 (14.2.0-6) ... Setting up libc6:arm64 (2.40-3) ... Setting up libhwasan0:arm64 (14.2.0-6) ... Setting up libasan8:arm64 (14.2.0-6) ... Setting up libtsan2:arm64 (14.2.0-6) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1) ... Setting up libstdc++6:arm64 (14.2.0-6) ... Setting up liblsan0:arm64 (14.2.0-6) ... Setting up libitm1:arm64 (14.2.0-6) ... Setting up libcrypt1:arm64 (1:4.4.36-5) ... Setting up libgomp1:arm64 (14.2.0-6) ... Setting up libsquid-dev:arm64 (1.9g+cvs20050121-15.1) ... Setting up libatomic1:arm64 (14.2.0-6) ... Setting up libubsan1:arm64 (14.2.0-6) ... Setting up libcrypt-dev:arm64 (1:4.4.36-5) ... Setting up libc6-dev:arm64 (2.40-3) ... Setting up libgcc-14-dev:arm64 (14.2.0-6) ... Setting up libstdc++-14-dev:arm64 (14.2.0-6) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.40-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-6 gcc-14_14.2.0-6 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-6 libstdc++-14-dev-arm64-cross_14.2.0-6cross1 libstdc++6_14.2.0-6 libstdc++6-arm64-cross_14.2.0-6cross1 linux-libc-dev_6.11.2-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 binutils-x86-64-linux-gnu_2.43.1-5 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.2.0-1 cpp-14_14.2.0-6 cpp-14-aarch64-linux-gnu_14.2.0-6cross1 cpp-14-x86-64-linux-gnu_14.2.0-6 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-arm64_12.12 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-exec_0.30 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-6 g++-14-aarch64-linux-gnu_14.2.0-6cross1 g++-14-x86-64-linux-gnu_14.2.0-6 g++-aarch64-linux-gnu_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-6 gcc-14-aarch64-linux-gnu_14.2.0-6cross1 gcc-14-aarch64-linux-gnu-base_14.2.0-6cross1 gcc-14-base_14.2.0-6 gcc-14-cross-base_14.2.0-6cross1 gcc-14-x86-64-linux-gnu_14.2.0-6 gcc-aarch64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gpgv_2.2.44-1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.25 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-6 libasan8-arm64-cross_14.2.0-6cross1 libatomic1_14.2.0-6 libatomic1-arm64-cross_14.2.0-6cross1 libattr1_1:2.5.2-2 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-5 libblkid1_2.40.2-9 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-3 libc-dev-bin_2.40-3 libc6_2.40-3 libc6-arm64-cross_2.40-3cross1 libc6-dev_2.40-3 libc6-dev-arm64-cross_2.40-3cross1 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-6 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libdb5.3t64_5.3.28+dfsg2-8 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libelf1t64_0.191-2 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-14-dev_14.2.0-6 libgcc-14-dev-arm64-cross_14.2.0-6cross1 libgcc-s1_14.2.0-6 libgcc-s1-arm64-cross_14.2.0-6cross1 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-6 libgomp1-arm64-cross_14.2.0-6cross1 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libhogweed6t64_3.10-1 libhwasan0_14.2.0-6 libhwasan0-arm64-cross_14.2.0-6cross1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-6 libitm1-arm64-cross_14.2.0-6cross1 libjansson4_2.14-2+b2 liblsan0_14.2.0-6 liblsan0-arm64-cross_14.2.0-6cross1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-9 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libnettle8t64_3.10-1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl4-corelibs-perl_0.005-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-6 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-3 libquadmath0_14.2.0-6 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-5 libsmartcols1_2.40.2-9 libsquid-dev_1.9g+cvs20050121-15.1 libsquid1t64_1.9g+cvs20050121-15.1 libssl3t64_3.3.2-1 libstdc++-14-dev_14.2.0-6 libstdc++-14-dev-arm64-cross_14.2.0-6cross1 libstdc++6_14.2.0-6 libstdc++6-arm64-cross_14.2.0-6cross1 libsystemd0_256.7-1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-6 libtsan2-arm64-cross_14.2.0-6cross1 libubsan1_14.2.0-6 libubsan1-arm64-cross_14.2.0-6cross1 libuchardet0_0.0.8-1+b1 libudev1_256.7-1 libunistring5_1.2-1 libuuid1_2.40.2-9 libxml2_2.12.7+dfsg+really2.9.14-0.1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.11.2-1 linux-libc-dev-arm64-cross_6.11.2-1cross1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 mount_2.40.2-9 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-6 perl-base_5.40.0-6 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-6 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 rename_2.02-1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 tzdata_2024b-3 usr-is-merged_39 util-linux_2.40.2-9 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hmmer2 Binary: hmmer2, hmmer2-doc, libhmmer2-dev Architecture: any all Version: 2.3.2+dfsg-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://hmmer.janelia.org/ Standards-Version: 4.7.0 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, pkgconf, 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 062cd885dfd33766c3303b641a9fd2ad123990c4 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz Checksums-Sha256: f9cd50acc23743648cb7de020c249bce396c3d07e0afe7e5418620cffa07bb44 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 1dd6e7702c9a6540fd8a3b53d535c98e822a7dfdbc76388f81b0cdc731e42f2a 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz Files: 4f8c9fd7c7de00fb8cfab499931ee4ba 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 5d8ec6eb7213aa0fc5ec00a3be5af26b 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYXp30RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH0rQ/+Nx0cD07oRQUQX/qMb9hbDYgoC5X3s6BG t7cMJgk6/qDEClluc58uQZSVDYFLr2NDaWWf6Avh5vcwGsgiimmU99tV4eu2B2tT 5s7zx6HwEOHLtdsYDGJnPpuNUhiE1wOvzXcabZ9t8PpCRe3ZUkFkmyvSsPXrMdtX SZapCF6fbBB2AG/5JVCYJxrb4BLBxffeLl0/7YsxFaLi0Hm9k49yB9w5K7FTn+9G EmvpkpT0rHVlalEIcZNsHJ8DIfPAcN9DKRL+FxDgh1Z0TNRVQdZ7kS/72QdloAzS QPml++aDp4iI6H0s1RDHfGqJ3d5Ootz/aDktgPUmHH84+WCtTHQkQrJQuQpRfS9i UeORZNpEOpezcVR8aaYlDQTx42O+oeKC3OCYZRZkgEu64uH6zlqRijA1bfUCy/NS UglYqpYqppQBMmUDTy0d3DFk92mSM0EyWz/bN8ton0oyYXwdmjF/Jp774gZLJ5Yw xG7exdw2efasNYcMklZQ2lbrX0ClYu5mC2A+zpuGNL1TnCn3hLNh6Lx1uwZuG4xz 98NPhg6ttguogyizeEpEedDzxwUIhsDWnyr126PIynIIXj0PluqnLI2MKtwfGU6z KRFdTbBUpn83qmm7AHQWGQ0dihSVqgFne4IhuyQ4f93INpqxYKwFtDcBR8veJy8+ P8gYNfTK1/w= =SERy -----END PGP SIGNATURE----- gpgv: Signature made Thu Apr 11 09:03:57 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-12.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-12.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 dpkg-source: info: applying fixup-implicit-function-declaration.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.xeJAeWcn9I/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-919bdb1e-8968-4cb5-81a2-143fdd0d9473 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean if [ -e configure_not_used ] ; then mv configure_not_used configure; fi rm -f configure.ac src/config.h make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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:119: warning: underquoted definition of CHECK_GNU_MAKE configure.ac:119: run info Automake 'Extending aclocal' configure.ac:119: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:161: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:161: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:161: the top level configure.ac:487: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level configure.ac:487: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm ./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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=aarch64-linux-gnu --enable-threads --enable-lfs PTHREAD_CFLAGS=-D_XOPEN_SOURCE=500 configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for aarch64-linux-gnu-gcc... aarch64-linux-gnu-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... yes checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether aarch64-linux-gnu-gcc accepts -g... yes checking for aarch64-linux-gnu-gcc option to enable C11 features... none needed checking for aarch64-linux-gnu-ranlib... aarch64-linux-gnu-ranlib checking for ar... /usr/bin/ar checking for aarch64-linux-gnu-pkg-config... /usr/bin/aarch64-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking build system type... x86_64-pc-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 pthread_join in LIBS= with CFLAGS=-D_XOPEN_SOURCE=500... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... aarch64-linux-gnu-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 -j1 make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/src' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmalign.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c alphabet.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c core_algorithms.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c debug.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c display.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c emit.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c emulation.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c fast_algorithms.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c histogram.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmio.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c mathsupport.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c masks.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c misc.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c modelmakers.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c plan7.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c plan9.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c postprob.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c prior.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c pvm.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c threads.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c tophits.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c trace.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmbuild.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmcalibrate.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmconvert.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmemit.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmfetch.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmindex.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmpfam.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -c hmmsearch.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -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 `/usr/bin/aarch64-linux-gnu-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 aarch64-linux-gnu-ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/testsuite' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c alignalign_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c evd_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c masks_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c tophits_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c trace_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/aarch64-linux-gnu-pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/aarch64-linux-gnu-pkg-config --libs libsquid` -lm 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 -j1 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 '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' sed -e "s/@DEB_HOST_MULTIARCH@/aarch64-linux-gnu/" \ -e "s/@VERSION@/2.3.2/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc dh_install rm -f debian/pkgconfig/libhmmer2.pc make[1]: Leaving directory '/<>' 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 '/<>' cd testsuite && make clean && cd .. 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' dh_installexamples mkdir -p /<>/debian/hmmer2/usr/share/doc/hmmer2/examples; 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#hmm#hmm2#g" /<>/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc 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 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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 dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. dpkg-genbuildinfo --build=any -O../hmmer2_2.3.2+dfsg-12_arm64.buildinfo dpkg-genchanges --build=any -O../hmmer2_2.3.2+dfsg-12_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 2024-10-14T21:04:39Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ hmmer2_2.3.2+dfsg-12_arm64.changes: ----------------------------------- Format: 1.8 Date: Thu, 11 Apr 2024 09:59:24 +0200 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym libhmmer2-dev Built-For-Profiles: cross nocheck Architecture: arm64 Version: 2.3.2+dfsg-12 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team 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 Changes: hmmer2 (2.3.2+dfsg-12) unstable; urgency=medium . * Drop -fcf-protection=full option in autoplgtest which works on amd64+i386 only and makes the test fail on other architectures * Drop emeritus Laszlo Kajan from Uploaders (thanks for all your work Laszlo) * Standards-Version: 4.7.0 (routine-update) * Use secure URI in Homepage field. * Remove patch hardening.patch that is missing from debian/patches/series. * DEP3 + Forwarded: No Checksums-Sha1: 286d3946dbcd3822b85fe442a05625868e06e1aa 1227724 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb 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2d1892058f340e77ec6adf6db2e3446a 91864 libdevel optional libhmmer2-dev_2.3.2+dfsg-12_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym libhmmer2-dev Architecture: arm64 Version: 2.3.2+dfsg-12 Checksums-Md5: 848d1e4a12215cefd70282321d962780 1227724 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb ac5c8c8e5f7b130287770470d963bddb 288404 hmmer2_2.3.2+dfsg-12_arm64.deb 2d1892058f340e77ec6adf6db2e3446a 91864 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Checksums-Sha1: 286d3946dbcd3822b85fe442a05625868e06e1aa 1227724 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb 8e9497336ffc70c37fa1ae430132e1f5ac356617 288404 hmmer2_2.3.2+dfsg-12_arm64.deb f247272489ab4bb32936b90932c05c1ddf568a5b 91864 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Checksums-Sha256: 08c835537ec3fbf8fc73d659bfd30a0e31b7e2063dc556796a9e67eafdac3a08 1227724 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb 2146df8b7969172307dcf17b10279e819fd16594f63bcc3b21d75e0937dc95a3 288404 hmmer2_2.3.2+dfsg-12_arm64.deb b2ad92c9c8557f57903233a6ea1c381344cf6760769777c7e9bf104f17b92541 91864 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 14 Oct 2024 21:04:38 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-5), binutils-common (= 2.43.1-5), binutils-x86-64-linux-gnu (= 2.43.1-5), bsdextrautils (= 2.40.2-9), bsdutils (= 1:2.40.2-9), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-6), cpp-14-x86-64-linux-gnu (= 14.2.0-6), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-exec (= 0.30), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-6), g++-14-x86-64-linux-gnu (= 14.2.0-6), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-6), gcc-14-base (= 14.2.0-6), gcc-14-x86-64-linux-gnu (= 14.2.0-6), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.25), init-system-helpers (= 1.67), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-6), libatomic1 (= 14.2.0-6), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43.1-5), libblkid1 (= 2.40.2-9), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-3), libc-dev-bin (= 2.40-3), libc6 (= 2.40-3), libc6-dev (= 2.40-3), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-6), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-5), libctf0 (= 2.43.1-5), libdb5.3t64 (= 5.3.28+dfsg2-8), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-14-dev (= 14.2.0-6), libgcc-s1 (= 14.2.0-6), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-6), libgprofng0 (= 2.43.1-5), libhwasan0 (= 14.2.0-6), libicu72 (= 72.1-5), libisl23 (= 0.27-1), libitm1 (= 14.2.0-6), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.2.0-6), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-9), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl4-corelibs-perl (= 0.005-1), libperl5.40 (= 5.40.0-6), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-3), libquadmath0 (= 14.2.0-6), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-5), libsmartcols1 (= 2.40.2-9), libsquid-dev (= 1.9g+cvs20050121-15.1), libsquid1t64 (= 1.9g+cvs20050121-15.1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-6), libstdc++6 (= 14.2.0-6), libsystemd0 (= 256.7-1), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-6), libubsan1 (= 14.2.0-6), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.7-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-9), libxml2 (= 2.12.7+dfsg+really2.9.14-0.1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.11.2-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-6), perl-base (= 5.40.0-6), perl-modules-5.40 (= 5.40.0-6), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), rename (= 2.02-1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-2), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-9), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1712822364" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb ------------------------------------- new Debian package, version 2.0. size 1227724 bytes: control archive=1004 bytes. 707 bytes, 12 lines control 1038 bytes, 10 lines md5sums Package: hmmer2-dbgsym Source: hmmer2 Version: 2.3.2+dfsg-12 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 1500 Depends: hmmer2 (= 2.3.2+dfsg-12) Section: debug Priority: optional Description: debug symbols for hmmer2 Build-Ids: 1389ba671a11f62f9f8dd70cdce3dc94f83fb1a6 2962a6522a5f1b51d94dc6dee38f8f00f6089758 2df9815cd954424ba3dc0550a6867ee2c378a8dc 4a7f71b6d3651ff3b08cdefdff8e09ebea451bc0 58740446c15621fd624dee73fe69f160a25fc2bb 6b60c604101a26cffe450d5760d2b954e57e43b7 9ad8f69dad0b560220645318365acef51e7575eb da9ddfe3e4c84c09ce027a0e6f92ce5caefbd9cd f337cd7127a424ac30deb86b39415052a849056e drwxr-xr-x root/root 0 2024-04-11 07:59 ./ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/13/ -rw-r--r-- root/root 163992 2024-04-11 07:59 ./usr/lib/debug/.build-id/13/89ba671a11f62f9f8dd70cdce3dc94f83fb1a6.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/29/ -rw-r--r-- root/root 168920 2024-04-11 07:59 ./usr/lib/debug/.build-id/29/62a6522a5f1b51d94dc6dee38f8f00f6089758.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/2d/ -rw-r--r-- root/root 170376 2024-04-11 07:59 ./usr/lib/debug/.build-id/2d/f9815cd954424ba3dc0550a6867ee2c378a8dc.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/4a/ -rw-r--r-- root/root 163032 2024-04-11 07:59 ./usr/lib/debug/.build-id/4a/7f71b6d3651ff3b08cdefdff8e09ebea451bc0.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/58/ -rw-r--r-- root/root 174832 2024-04-11 07:59 ./usr/lib/debug/.build-id/58/740446c15621fd624dee73fe69f160a25fc2bb.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/6b/ -rw-r--r-- root/root 160312 2024-04-11 07:59 ./usr/lib/debug/.build-id/6b/60c604101a26cffe450d5760d2b954e57e43b7.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/9a/ -rw-r--r-- root/root 161672 2024-04-11 07:59 ./usr/lib/debug/.build-id/9a/d8f69dad0b560220645318365acef51e7575eb.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/da/ -rw-r--r-- root/root 162168 2024-04-11 07:59 ./usr/lib/debug/.build-id/da/9ddfe3e4c84c09ce027a0e6f92ce5caefbd9cd.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.build-id/f3/ -rw-r--r-- root/root 169352 2024-04-11 07:59 ./usr/lib/debug/.build-id/f3/37cd7127a424ac30deb86b39415052a849056e.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/debug/.dwz/aarch64-linux-gnu/ -rw-r--r-- root/root 16384 2024-04-11 07:59 ./usr/lib/debug/.dwz/aarch64-linux-gnu/hmmer2.debug drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-04-11 07:59 ./usr/share/doc/hmmer2-dbgsym -> hmmer2 hmmer2_2.3.2+dfsg-12_arm64.deb ------------------------------ new Debian package, version 2.0. size 288404 bytes: control archive=2564 bytes. 849 bytes, 20 lines control 5091 bytes, 69 lines md5sums Package: hmmer2 Version: 2.3.2+dfsg-12 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 2389 Depends: libc6 (>= 2.34), libsquid1t64 (>= 1.9g+cvs20050121) Recommends: biosquid Suggests: hmmer2-doc (>= 2.3.2+dfsg-12) Section: science Priority: optional Homepage: https://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 2024-04-11 07:59 ./ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/bin/ -rwxr-xr-x root/root 199784 2024-04-11 07:59 ./usr/bin/hmm2align -rwxr-xr-x root/root 201896 2024-04-11 07:59 ./usr/bin/hmm2build -rwxr-xr-x root/root 199696 2024-04-11 07:59 ./usr/bin/hmm2calibrate -rwxr-xr-x root/root 199568 2024-04-11 07:59 ./usr/bin/hmm2convert -rwxr-xr-x root/root 199488 2024-04-11 07:59 ./usr/bin/hmm2emit -rwxr-xr-x root/root 199200 2024-04-11 07:59 ./usr/bin/hmm2fetch -rwxr-xr-x root/root 199112 2024-04-11 07:59 ./usr/bin/hmm2index -rwxr-xr-x root/root 200592 2024-04-11 07:59 ./usr/bin/hmm2pfam -rwxr-xr-x root/root 200384 2024-04-11 07:59 ./usr/bin/hmm2search drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/hmmer2/ lrwxrwxrwx root/root 0 2024-04-11 07:59 ./usr/lib/hmmer2/hmmindex -> ../../bin/hmm2index lrwxrwxrwx root/root 0 2024-04-11 07:59 ./usr/lib/hmmer2/hmmpfam -> ../../bin/hmm2pfam drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/hmmer2/ -rw-r--r-- root/root 2293 2024-04-11 07:59 ./usr/share/doc/hmmer2/00README lrwxrwxrwx root/root 0 2024-04-11 07:59 ./usr/share/doc/hmmer2/NOTES.gz -> changelog.gz -rw-r--r-- root/root 615 2024-04-11 07:59 ./usr/share/doc/hmmer2/README.Debian -rw-r--r-- root/root 1226 2024-04-11 07:59 ./usr/share/doc/hmmer2/changelog.Debian.gz -rw-r--r-- root/root 2161 2024-04-11 07:59 ./usr/share/doc/hmmer2/changelog.gz -rw-r--r-- root/root 1411 2024-04-11 07:59 ./usr/share/doc/hmmer2/copyright drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/hmmer2/examples/ -rw-r--r-- root/root 1985 2024-04-11 07:59 ./usr/share/doc/hmmer2/examples/Makefile -rw-r--r-- root/root 1757 2024-04-11 07:59 ./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 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/evd_test.c -rw-r--r-- root/root 592 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/exercises-pvm.sqc -rw-r--r-- root/root 548 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/exercises-threaded.sqc -rw-r--r-- root/root 10522 2024-04-11 07:59 ./usr/share/doc/hmmer2/examples/exercises.sqc -rw-r--r-- root/root 1611 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/fitting_test.c -rw-r--r-- root/root 16930 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/fn3-bin -rw-r--r-- root/root 16930 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/fn3-bin-swap -rw-r--r-- root/root 31906 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/fn3.hmm -rw-r--r-- root/root 20514 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/fn3.seed -rw-r--r-- root/root 3926 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/masks_test.c -rw-r--r-- root/root 5491 2003-10-04 19:01 ./usr/share/doc/hmmer2/examples/parsingviterbi_test.c -rwxr-xr-x root/root 17674 2003-10-04 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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 2024-04-11 07:59 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/man/man1/ -rw-r--r-- root/root 1748 2024-04-11 07:59 ./usr/share/man/man1/hmm2align.1.gz -rw-r--r-- root/root 4765 2024-04-11 07:59 ./usr/share/man/man1/hmm2build.1.gz -rw-r--r-- root/root 1703 2024-04-11 07:59 ./usr/share/man/man1/hmm2calibrate.1.gz -rw-r--r-- root/root 1113 2024-04-11 07:59 ./usr/share/man/man1/hmm2convert.1.gz -rw-r--r-- root/root 1364 2024-04-11 07:59 ./usr/share/man/man1/hmm2emit.1.gz -rw-r--r-- root/root 945 2024-04-11 07:59 ./usr/share/man/man1/hmm2fetch.1.gz -rw-r--r-- root/root 752 2024-04-11 07:59 ./usr/share/man/man1/hmm2index.1.gz -rw-r--r-- root/root 3395 2024-04-11 07:59 ./usr/share/man/man1/hmm2pfam.1.gz -rw-r--r-- root/root 3046 2024-04-11 07:59 ./usr/share/man/man1/hmm2search.1.gz -rw-r--r-- root/root 1691 2024-04-11 07:59 ./usr/share/man/man1/hmmer2.1.gz libhmmer2-dev_2.3.2+dfsg-12_arm64.deb ------------------------------------- new Debian package, version 2.0. size 91864 bytes: control archive=1108 bytes. 876 bytes, 22 lines control 696 bytes, 10 lines md5sums Package: libhmmer2-dev Source: hmmer2 Version: 2.3.2+dfsg-12 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 332 Section: libdevel Priority: optional Multi-Arch: same Homepage: https://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 2024-04-11 07:59 ./ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/include/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/include/hmmer2/ -rw-r--r-- root/root 4524 2024-04-11 07:59 ./usr/include/hmmer2/config.h -rw-r--r-- root/root 16177 2024-04-11 07:59 ./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 2024-04-11 07:59 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/aarch64-linux-gnu/ -rw-r--r-- root/root 267776 2024-04-11 07:59 ./usr/lib/aarch64-linux-gnu/libhmmer.a drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/lib/aarch64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 263 2024-04-11 07:59 ./usr/lib/aarch64-linux-gnu/pkgconfig/libhmmer2.pc drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-11 07:59 ./usr/share/doc/libhmmer2-dev/ lrwxrwxrwx root/root 0 2024-04-11 07:59 ./usr/share/doc/libhmmer2-dev/NOTES.gz -> changelog.gz -rw-r--r-- root/root 1231 2024-04-11 07:59 ./usr/share/doc/libhmmer2-dev/changelog.Debian.gz -rw-r--r-- root/root 2161 2024-04-11 07:59 ./usr/share/doc/libhmmer2-dev/changelog.gz -rw-r--r-- root/root 1411 2024-04-11 07:59 ./usr/share/doc/libhmmer2-dev/copyright lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1360 B] Get:5 copy:/<>/apt_archive ./ Packages [1439 B] Fetched 3414 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The solver encountered an error of type: ERR_UNSOLVABLE The following information might help you to understand what is wrong: Unsatisfied dependencies: libnetaddr-ip-perl : Depends: perlapi-5.38.2 but it is not installable libvariable-magic-perl : Depends: perlapi-5.38.2 but it is not installable libnet-ssleay-perl : Depends: perlapi-5.38.2 but it is not installable libsereal-decoder-perl : Depends: perlapi-5.38.2 but it is not installable libdevel-size-perl : Depends: perlapi-5.38.2 but it is not installable libsyntax-keyword-try-perl : Depends: perlapi-5.38.2 but it is not installable Depends: libxs-parse-keyword-perl (>= 0.35) but it is not going to be installed libclass-xsaccessor-perl : Depends: perlapi-5.38.2 but it is not installable Depends: perl (< 5.38.3~) but 5.40.0-6 is to be installed libtext-markdown-discount-perl : Depends: perlapi-5.38.2 but it is not installable libsereal-encoder-perl : Depends: perlapi-5.38.2 but it is not installable libterm-readkey-perl : Depends: perlapi-5.38.2 but it is not installable libperlio-utf8-strict-perl : Depends: perlapi-5.38.2 but it is not installable libtext-xslate-perl : Depends: perlapi-5.38.2 but it is not installable Depends: libdata-messagepack-perl but it is not going to be installed Depends: libmouse-perl but it is not going to be installed libparams-classify-perl : Depends: libdevel-callchecker-perl but it is not going to be installed Depends: perlapi-5.38.2 but it is not installable libhtml-parser-perl : Depends: perlapi-5.38.2 but it is not installable libsub-identify-perl : Depends: perlapi-5.38.2 but it is not installable libberkeleydb-perl : Depends: perlapi-5.38.2 but it is not installable libunicode-utf8-perl : Depends: perlapi-5.38.2 but it is not installable libparams-util-perl : Depends: perlapi-5.38.2 but it is not installable libtime-moment-perl : Depends: perlapi-5.38.2 but it is not installable libemail-address-xs-perl : Depends: perlapi-5.38.2 but it is not installable libclone-perl : Depends: perlapi-5.38.2 but it is not installable libyaml-libyaml-perl : Depends: perlapi-5.38.2 but it is not installable libtext-levenshteinxs-perl : Depends: perlapi-5.38.2 but it is not installable libxml-libxml-perl : Depends: perlapi-5.38.2 but it is not installable libcpanel-json-xs-perl : Depends: perlapi-5.38.2 but it is not installable libperlio-gzip-perl : Depends: perlapi-5.38.2 but it is not installable libsub-name-perl : Depends: perlapi-5.38.2 but it is not installable libapt-pkg-perl : Depends: perlapi-5.38.2 but it is not installable libproc-processtable-perl : Depends: perlapi-5.38.2 but it is not installable Execute external solver... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: sbuild-build-depends-lintian-dummy:arm64 : Depends: lintian:amd64 E: External solver failed with: Unsatisfied dependencies: apt-get failed. E: Package installation failed Not removing build depends: cloned chroot in use +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 22296 Build-Time: 17 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 10 Job: hmmer2_2.3.2+dfsg-12 Lintian: error Machine Architecture: amd64 Package: hmmer2 Package-Time: 38 Source-Version: 2.3.2+dfsg-12 Space: 22296 Status: successful Version: 2.3.2+dfsg-12 -------------------------------------------------------------------------------- Finished at 2024-10-14T21:04:39Z Build needed 00:00:38, 22296k disk space