sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | hmmer 3.4+dfsg-3 (amd64) Sat, 19 Sep 2026 23:52:08 +0000 | +==============================================================================+ Package: hmmer Version: 3.4+dfsg-3 Source Version: 3.4+dfsg-3 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sat, 19 Sep 2026 23:52:10 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hmmer_3.4+dfsg-3 perl-5.44-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hmmer_3.4+dfsg-3 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 19 Sep 2026 23:52:10 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sat, 19 Sep 2026 23:52:14 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/hmmer_3.4+dfsg-3.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 19 Sep 2026 23:52:15 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, python3, build-essential Filtered Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, python3, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ InRelease Get:2 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ Release [609 B] Ign:3 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ Release.gpg Get:4 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ Sources [628 B] Get:5 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ Packages [667 B] Fetched 1904 B in 0s (118 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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdivsufsort-dev libdivsufsort3 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libtool libuchardet0 libxml2-16 m4 man-db media-types netbase po-debconf python3 python3-minimal python3.14 python3.14-minimal sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binfmt-support Recommended packages: curl | wget | lynx python3-requests libarchive-cpio-perl libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdivsufsort-dev libdivsufsort3 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libtool libuchardet0 libxml2-16 m4 man-db media-types netbase po-debconf python3 python3-minimal python3.14 python3.14-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After this operation, 82.7 MB of additional disk space will be used. Get:1 copy:/build/hmmer-2ml2gJ/resolver-DWXGat/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [876 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.4-1 [130 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.7-4 [902 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.7-4 [2713 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.7-3 [25.3 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.6 [10.3 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026c-1 [260 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.7-4 [2362 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.7-4 [861 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.7-3 [8252 B] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.7-3 [26.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-5 [334 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.3-1 [102 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.19-2 [891 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-5 [820 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.5 [77.7 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtool all 2.6.2-3 [552 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 23 [12.7 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.196-1 [61.2 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.4+dfsg-1 [683 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-5 [2704 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.5 [944 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-7+b1 [46.1 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-7+b1 [19.1 kB] Preconfiguring packages ... Fetched 19.4 MB in 0s (128 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 15722 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.4-1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.7-4_amd64.deb ... Unpacking libpython3.14-minimal:amd64 (3.14.7-4) ... Selecting previously unselected package python3.14-minimal. Preparing to unpack .../python3.14-minimal_3.14.7-4_amd64.deb ... Unpacking python3.14-minimal (3.14.7-4) ... Setting up libpython3.14-minimal:amd64 (3.14.7-4) ... Setting up libexpat1:amd64 (2.8.4-1) ... Setting up python3.14-minimal (3.14.7-4) ... Selecting previously unselected package python3-minimal. (Reading database ... 16078 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.14.7-3_amd64.deb ... Unpacking python3-minimal (3.14.7-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.6_all.deb ... Unpacking netbase (6.6) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2026c-1_all.deb ... Unpacking tzdata (2026c-1) ... Selecting previously unselected package libpython3.14-stdlib:amd64. Preparing to unpack .../4-libpython3.14-stdlib_3.14.7-4_amd64.deb ... Unpacking libpython3.14-stdlib:amd64 (3.14.7-4) ... Selecting previously unselected package python3.14. Preparing to unpack .../5-python3.14_3.14.7-4_amd64.deb ... Unpacking python3.14 (3.14.7-4) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.14.7-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.14.7-3) ... Setting up python3-minimal (3.14.7-3) ... Selecting previously unselected package python3. (Reading database ... 17066 files and directories currently installed.) Preparing to unpack .../00-python3_3.14.7-3_amd64.deb ... Unpacking python3 (3.14.7-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_1.0-5_amd64.deb ... Unpacking gettext-base (1.0-5) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.42.3-1_amd64.deb ... Unpacking bsdextrautils (2.42.3-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.73-2_all.deb ... Unpacking autoconf (2.73-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1+nmu1_all.deb ... Unpacking autotools-dev (20240727.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.19-2_all.deb ... Unpacking automake (1:1.19-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_1.0-5_all.deb ... Unpacking autopoint (1.0-5) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_14.5_all.deb ... Unpacking libdebhelper-perl (14.5) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.6.2-3_all.deb ... Unpacking libtool (2.6.2-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_23_all.deb ... Unpacking dh-autoreconf (23) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.15.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.15.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.196-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.196-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.17-1_amd64.deb ... Unpacking dwz (0.17-1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.15.4+dfsg-1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.4+dfsg-1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_1.0-5_amd64.deb ... Unpacking gettext (1.0-5) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.22_all.deb ... Unpacking po-debconf (1.0.22) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_14.5_all.deb ... Unpacking debhelper (14.5) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../29-libdivsufsort3_2.0.1-7+b1_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-7+b1) ... Selecting previously unselected package libdivsufsort-dev:amd64. Preparing to unpack .../30-libdivsufsort-dev_2.0.1-7+b1_amd64.deb ... Unpacking libdivsufsort-dev:amd64 (2.0.1-7+b1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../31-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up bsdextrautils (2.42.3-1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.4+dfsg-1) ... Setting up libdebhelper-perl (14.5) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up gettext-base (1.0-5) ... Setting up m4 (1.4.21-1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.196-1) ... Setting up tzdata (2026c-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 19 23:52:27 UTC 2026. Universal Time is now: Sat Sep 19 23:52:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up autopoint (1.0-5) ... Setting up autoconf (2.73-2) ... Setting up dwz (0.17-1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up netbase (6.6) ... Configuration file '/etc/services' ==> Modified locally since installation. ==> Package distributor has shipped an updated version. ==> Using current old file as requested. Setting up libdivsufsort3:amd64 (2.0.1-7+b1) ... Setting up libdivsufsort-dev:amd64 (2.0.1-7+b1) ... Setting up automake (1:1.19-2) ... update-alternatives: using /usr/bin/automake-1.19 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-5) ... Setting up libtool (2.6.2-3) ... Setting up libpython3.14-stdlib:amd64 (3.14.7-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (23) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up python3.14 (3.14.7-4) ... Setting up libpython3-stdlib:amd64 (3.14.7-3) ... Setting up po-debconf (1.0.22) ... Setting up python3 (3.14.7-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (14.5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.43-5) ... +------------------------------------------------------------------------------+ | Check architectures Sat, 19 Sep 2026 23:52:30 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sat, 19 Sep 2026 23:52:30 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-15_15.3.0-4 g++-16_16.2.0-3 gcc-15_15.3.0-4 gcc-16_16.2.0-3 libc6-dev_2.43-5 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 linux-libc-dev_7.2.6-1 Package versions: apt_3.3.3 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-4 binutils_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.3-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-15_15.3.0-4 cpp-15-x86-64-linux-gnu_15.3.0-4 cpp-16_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 dash_0.5.12-12 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7+b1 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 eatmydata_131-2 file_1:5.47-4 findutils_4.11.0-2 g++_4:16.1.0-3 g++-15_15.3.0-4 g++-15-x86-64-linux-gnu_15.3.0-4 g++-16_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-15_15.3.0-4 gcc-15-base_15.3.0-4 gcc-15-x86-64-linux-gnu_15.3.0-4 gcc-16_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-x86-64-linux-gnu_16.2.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7+b1 gpg-agent_2.4.9-7+b1 gpgconf_2.4.9-7+b1 gpgsm_2.4.9-7+b1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.14-1 hostname_3.25 init-system-helpers_1.69+nmu1 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libassuan9_3.0.2-2+b2 libatomic1_16.2.0-3 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b2 libbinutils_2.47-6 libblkid1_2.42.3-1 libbz2-1.0_1.0.8-6+b2 libc-bin_2.43-5 libc-dev-bin_2.43-5 libc-gconv-modules-extra_2.43-5 libc6_2.43-5 libc6-dev_2.43-5 libcap-ng0_0.9.6-1 libcc1-0_16.2.0-3 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdivsufsort-dev_2.0.1-7+b1 libdivsufsort3_2.0.1-7+b1 libdpkg-perl_1.23.11 libeatmydata1_131-2+b2 libelf1t64_0.196-1 libexpat1_2.8.4-1 libffi8_3.8.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-4 libgcc-16-dev_16.2.0-3 libgcc-s1_16.2.0-3 libgcrypt20_1.12.3-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgpg-error0_1.61-5 libgprofng0_2.47-6 libhogweed6t64_3.10.2-1+b1 libhwasan0_16.2.0-3 libidn2-0_2.3.8-5 libisl23_0.28-1 libitm1_16.2.0-3 libjansson4_2.15.1-1 libksba8_1.8.1-1 libldap2_2.6.14+dfsg-2+b1 liblsan0_16.2.0-3 liblz4-1_1.10.0-10 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.3-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-4 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.48-3 libperl5.40_5.40.1-8 libperl5.44_5.44.0-1 libpipeline1_1.5.8-3 libpython3-stdlib_3.14.7-3 libpython3.14-minimal_3.14.7-4 libpython3.14-stdlib_3.14.7-4 libquadmath0_16.2.0-3 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1+b1 libselinux1_3.11-2 libsframe3_2.47-6 libsmartcols1_2.42.3-1 libsqlite3-0_3.53.4-2 libssl3t64_3.6.4-1 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 libsystemd0_262~rc3-1 libtasn1-6_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtss2-mu-4.0.1-0t64_4.1.3-7 libtss2-rc0t64_4.1.3-7 libtss2-sys1t64_4.1.3-7 libtss2-tcti-device0t64_4.1.3-7 libtss2-tcti-mssim0t64_4.1.3-7 libtss2-tcti-swtpm0t64_4.1.3-7 libubsan1_16.2.0-3 libuchardet0_0.0.8-2+b2 libudev1_262~rc3-1 libunistring5_1.4.2-1 libuuid1_2.42.3-1 libxml2-16_2.15.4+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.6-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.42.3-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.6 openssl-provider-legacy_3.6.4-1 patch_2.8-2 perl_5.44.0-1 perl-base_5.44.0-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0-1 pinentry-curses_1.3.3-3 po-debconf_1.0.22 python3_3.14.7-3 python3-minimal_3.14.7-3 python3.14_3.14.7-4 python3.14-minimal_3.14.7-4 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-6 tzdata_2026c-1 util-linux_2.42.3-1 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sat, 19 Sep 2026 23:52:30 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hmmer Binary: hmmer, hmmer-doc, hmmer-examples Architecture: any all Version: 3.4+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://hmmer.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/hmmer Vcs-Git: https://salsa.debian.org/med-team/hmmer.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, python3 Package-List: hmmer deb science optional arch=any-amd64,any-i386,arm64,powerpc,ppc64,x32 hmmer-doc deb doc optional arch=all hmmer-examples deb doc optional arch=any Checksums-Sha1: 69590adb499ca8e4eea9d2ed10fb66ae42e82ea8 13297988 hmmer_3.4+dfsg.orig.tar.xz 1996bb01d664abff34eac52b5b57ef7e11d4a714 12996 hmmer_3.4+dfsg-3.debian.tar.xz Checksums-Sha256: 87ada77366ed6ab0159a0c1217f8a55cbe9a708c4a98cf644929eb3703ce3309 13297988 hmmer_3.4+dfsg.orig.tar.xz 3864769123ce5f52fca65a9fad242e1930dc813e28baca4d09075d143379deda 12996 hmmer_3.4+dfsg-3.debian.tar.xz Files: ac66418b48c613d96d43770f971a22d3 13297988 hmmer_3.4+dfsg.orig.tar.xz 1381e0ec563f438fa48b147b0c6b4335 12996 hmmer_3.4+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmjagNoACgkQQc5/C58b izIqwgf/aS9ZDyRa/dCnDzVTVu9pBa/OLznAAYdanFAIiePSuVO4ACAU6JjWB14d i/1ZByuuPl86dhdeqzR4NHbMJxaJH60KPXVZhKa2I5mrYlwD6upcD3HEwkGr/SyP xBdiTlxGIxoKiO3Ct8Hbz0b9T25uyfU45OOA6kVFpjg1wxiUUzxBjh5RKJFr6ZUR hBv/ctEvkE9D456Tu3o/LcyKmM4rQIhmY+UiBx5Srs/FSNYmPIq5nJCN/lTbUlIh KfWLtCB+dWHD5VERgyuQJN3m99VWW4BPZPvp1KTjBvS4SenF/bEzj83jvamAJqZs kTy9bmptwA1V+g2W8REqTnDzbmw6iQ== =qf5Q -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./hmmer_3.4+dfsg-3.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./hmmer_3.4+dfsg-3.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting hmmer in /build/hmmer-2ml2gJ/hmmer-3.4+dfsg dpkg-source: info: unpacking hmmer_3.4+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer_3.4+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_manpage_extension.patch dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying verbose-easel dpkg-source: info: applying skip_threads_check dpkg-source: info: applying sub_make_parallel dpkg-source: info: applying spelling clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sat, 19 Sep 2026 23:52:32 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hmmer_3.4+dfsg-3 perl-5.44-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hmmer_3.4+dfsg-3 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-fce8daa9-6f5a-427f-8269-4f852225a565 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package hmmer dpkg-buildpackage: info: source version 3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/source/options: --extend-diff-ignore=(^|/)config.(sub|guess)$ debian/rules clean dh clean debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' rm -f testsuite/esltmp* rm -f easel/testsuite/esltmp* rm -f tutorial/MADE1.hmm.h3? rm -f config.log config.status configure find . -name Makefile -delete make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using options from /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/source/options: --extend-diff-ignore=(^|/)config.(sub|guess)$ dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building hmmer using existing ../hmmer_3.4+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building hmmer in ../hmmer_3.4+dfsg-3.debian.tar.xz dpkg-source: info: building hmmer in ../hmmer_3.4+dfsg-3.dsc debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' AUTOHEADER=true dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force autoreconf: configure.ac: easel/decoy_config.h.in was not generated by autoheader autoreconf: force update of easel/decoy_config.h.in with --replace-handwritten autoreconf: configure.ac: not using Automake autoreconf: './install-sh' is updated autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" dh_auto_configure -- --enable-threads --enable-sse ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-sse configure: Configuring HMMER3 for your system. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether to compile using MPI... no checking for gcc... x86_64-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... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking for gcc... (cached) x86_64-linux-gnu-gcc checking whether the compiler supports GNU C... (cached) yes checking whether x86_64-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-linux-gnu-gcc option to enable C23 features... (cached) none needed checking how to run the C preprocessor... x86_64-linux-gnu-gcc -E checking for a BSD-compatible install... /usr/bin/install -c checking for strip... strip checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for a sed that does not truncate output... /usr/bin/sed checking for egrep -e... /usr/bin/grep -E checking whether x86_64-linux-gnu-gcc is Clang... no checking whether pthreads work with "-pthread" and "-lpthread"... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether x86_64-linux-gnu-gcc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for python3... yes checking for library containing clock_gettime... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for netinet/in.h... yes checking for sys/param.h... yes checking for sys/sysctl.h... no checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... yes checking for popen... yes checking for putenv... yes checking for strcasecmp... yes checking for strsep... yes checking for times... yes checking for getpid... yes checking for sysctl... no checking for sysconf... yes checking for getcwd... yes checking for chmod... yes checking for stat... yes checking for fstat... yes checking for erfc... no checking for library containing ntohs... none required checking for library containing ntohl... none required checking for library containing htons... none required checking for library containing htonl... none required checking for library containing socket... none required checking for library containing inet_pton... none required checking for declarations of fseeko and ftello... yes checking for x86_64-linux-gnu-gcc option to support large files... none needed configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating documentation/userguide/Makefile config.status: creating documentation/userguide/inclusions/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating documentation/userguide/titlepage.tex config.status: creating documentation/userguide/titlepage_daemon.tex config.status: creating documentation/userguide/copyright.tex config.status: creating documentation/man/alimask.man config.status: creating documentation/man/hmmalign.man config.status: creating documentation/man/hmmbuild.man config.status: creating documentation/man/hmmc2.man config.status: creating documentation/man/hmmconvert.man config.status: creating documentation/man/hmmemit.man config.status: creating documentation/man/hmmer.man config.status: creating documentation/man/hmmfetch.man config.status: creating documentation/man/hmmlogo.man config.status: creating documentation/man/hmmpgmd.man config.status: creating documentation/man/hmmpgmd_shard.man config.status: creating documentation/man/hmmpress.man config.status: creating documentation/man/hmmscan.man config.status: creating documentation/man/hmmsearch.man config.status: creating documentation/man/hmmsim.man config.status: creating documentation/man/hmmstat.man config.status: creating documentation/man/jackhmmer.man config.status: creating documentation/man/makehmmerdb.man config.status: creating documentation/man/nhmmer.man config.status: creating documentation/man/nhmmscan.man config.status: creating documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: linking src/impl_sse to src/impl HMMER configuration: compiler: x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread host: x86_64-pc-linux-gnu linker: -Wl,-z,relro -Wl,-z,now -flto libraries: -lpthread DP implementation: sse Now do 'make' to build HMMER, and optionally: 'make check' to run self tests, 'make install' to install programs and man pages, '(cd easel; make install)' to install Easel tools. make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_auto_build make -j2 make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' make -C easel all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c easel.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_alloc.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_alphabet.c easel.c: In function ‘esl_FileTail’: easel.c:1788:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1788 | lastslash = strrchr(path, eslDIRSLASH); | ^ easel.c: In function ‘esl_FileNewSuffix’: easel.c:1938:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1938 | lastdot = strrchr(filename, '.'); /* check for suffix to replace */ | ^ x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_arr2.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_arr3.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_bitfield.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_buffer.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_cluster.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_composition.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_cpu.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_dirichlet.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_distance.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_dmatrix.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_dsqdata.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_exponential.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_fileparser.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_gamma.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_gencode.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_getopts.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_gev.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_graph.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_gumbel.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_heap.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_histogram.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_hmm.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_huffman.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_hyperexp.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_iset.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_json.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_keyhash.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_lognormal.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_matrixops.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_mem.c esl_mem.c: In function ‘esl_memnewline’: esl_mem.c:486:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 486 | char *ptr = memchr(m, '\n', n); | ^~~~~~ x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_minimizer.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_mixdchlet.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_mixgev.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_mpi.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msa.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msacluster.c esl_msa.c: In function ‘esl_msa_SymConvert’: esl_msa.c:2774:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2774 | if ((sptr = strchr(oldsyms, msa->aseq[idx][apos])) != NULL) | ^ x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile2.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_a2m.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_afa.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_clustal.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_phylip.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_psiblast.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_selex.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msafile_stockholm.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msashuffle.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_msaweight.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_normal.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_paml.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_quicksort.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_random.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_rand64.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_randomseq.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_ratematrix.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_recorder.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_red_black.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_regexp.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_rootfinder.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_scorematrix.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_sq.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_sqio.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_sqio_ascii.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_sqio_ncbi.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_ssi.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_stack.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_stats.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_stopwatch.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_stretchexp.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_subcmd.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_threads.c esl_subcmd.c: In function ‘esl_subcmd_CreateDefaultApp’: esl_subcmd.c:53:28: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 53 | char *lastslash = strrchr(topcmd, '/'); | ^~~~~~~ x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_tree.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_varint.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_vectorops.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_weibull.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_workqueue.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_wuss.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_sse.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_avx.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_avx512.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_neon.c x86_64-linux-gnu-gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -c esl_vmx.c /usr/bin/ar -r libeasel.a easel.o esl_alloc.o esl_alphabet.o esl_arr2.o esl_arr3.o esl_bitfield.o esl_buffer.o esl_cluster.o esl_composition.o esl_cpu.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_dsqdata.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_gencode.o esl_getopts.o esl_gev.o esl_graph.o esl_gumbel.o esl_heap.o esl_histogram.o esl_hmm.o esl_huffman.o esl_hyperexp.o esl_iset.o esl_json.o esl_keyhash.o esl_lognormal.o esl_matrixops.o esl_mem.o esl_minimizer.o esl_mixdchlet.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msafile.o esl_msafile2.o esl_msafile_a2m.o esl_msafile_afa.o esl_msafile_clustal.o esl_msafile_phylip.o esl_msafile_psiblast.o esl_msafile_selex.o esl_msafile_stockholm.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_quicksort.o esl_random.o esl_rand64.o esl_randomseq.o esl_ratematrix.o esl_recorder.o esl_red_black.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_subcmd.o esl_threads.o esl_tree.o esl_varint.o esl_vectorops.o esl_weibull.o esl_workqueue.o esl_wuss.o esl_sse.o esl_avx.o esl_avx512.o esl_neon.o esl_vmx.o > /dev/null 2>&1 make -C miniapps all make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lpthread -lm esl-mixdchlet.c: In function ‘top_usage’: esl-mixdchlet.c:47:21: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 47 | char *lastslash = strrchr(topcmd, '/'); | ^~~~~~~ esl-mixdchlet.c: In function ‘top_help’: esl-mixdchlet.c:62:21: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 62 | char *lastslash = strrchr(topcmd, '/'); | ^~~~~~~ x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -lpthread -lm x86_64-linux-gnu-gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -c cmd_alistat.c x86_64-linux-gnu-gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -c cmd_downsample.c x86_64-linux-gnu-gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -c cmd_filter.c cmd_filter.c: In function ‘process_cmdline’: cmd_filter.c:128:28: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 128 | char *lastslash = strrchr(topcmd, '/'); | ^~~~~~~ x86_64-linux-gnu-gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -c cmd_index.c x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o easel easel.c cmd_alistat.o cmd_downsample.o cmd_filter.o cmd_index.o -leasel -lpthread -lm easel.c: In function ‘top_usage’: easel.c:58:21: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 58 | char *lastslash = strrchr(topcmd, '/'); | ^~~~~~~ make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' make -C src all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o alimask.o -c alimask.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o build.o -c build.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o cachedb.o -c cachedb.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o cachedb_shard.o -c cachedb_shard.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o emit.o -c emit.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o errors.o -c errors.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o evalues.o -c evalues.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o eweight.o -c eweight.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback_chk.o -c generic_fwdback_chk.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback_banded.o -c generic_fwdback_banded.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_null2.o -c generic_null2.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_msv.o -c generic_msv.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o h2_io.o -c h2_io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o heatmap.o -c heatmap.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmlogo.o -c hmmlogo.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdmstr_shard.o -c hmmdmstr_shard.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmd_search_status.o -c hmmd_search_status.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdutils.o -c hmmdutils.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmer.o -c hmmer.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o logsum.o -c logsum.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o modelconfig.o -c modelconfig.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o modelstats.o -c modelstats.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o mpisupport.o -c mpisupport.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o seqmodel.o -c seqmodel.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o tracealign.o -c tracealign.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_bg.o -c p7_bg.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_builder.o -c p7_builder.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_domain.o -c p7_domain.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gbands.o -c p7_gbands.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hit.o -c p7_hit.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmd_search_stats.o -c p7_hmmd_search_stats.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_prior.o -c p7_prior.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_profile.o -c p7_profile.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_trace.o -c p7_trace.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_general.o -c fm_general.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_sse.o -c fm_sse.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_ssv.o -c fm_ssv.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmalign.o -c hmmalign.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmemit.o -c hmmemit.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd_shard.o -c hmmpgmd_shard.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpress.o -c hmmpress.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmscan.o -c hmmscan.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmsim.o -c hmmsim.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmstat.o -c hmmstat.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o phmmer.o -c phmmer.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o nhmmer.o -c nhmmer.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmc2.o -c hmmc2.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c /usr/bin/ar -r libhmmer.a build.o cachedb.o cachedb_shard.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdmstr_shard.o hmmd_search_status.o hmmdwrkr.o hmmdwrkr_shard.o hmmdutils.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domain.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hit.o p7_hmm.o p7_hmmcache.o p7_hmmd_search_stats.o p7_hmmfile.o p7_hmmwindow.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 make -C impl_sse libhmmer-impl.stamp make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o decoding.o -c decoding.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o fwdback.o -c fwdback.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o io.o -c io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o ssvfilter.o -c ssvfilter.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o msvfilter.o -c msvfilter.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o null2.o -c null2.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o optacc.o -c optacc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o stotrace.o -c stotrace.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o vitfilter.o -c vitfilter.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_omx.o -c p7_omx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_oprofile.o -c p7_oprofile.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o mpi.o -c mpi.c /usr/bin/ar -r ../libhmmer.a decoding.o fwdback.o io.o ssvfilter.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1 make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lpthread -lm ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lpthread -lm ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lpthread -lm ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lpthread -lm make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' make -C profmark all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/profmark' x86_64-linux-gnu-gcc -I../easel -I../easel -I../src -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c x86_64-linux-gnu-gcc -I../easel -I../easel -I../src -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lpthread -lm x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lpthread -lm make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/profmark' make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' /usr/bin/make tests -j 2 make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' /usr/bin/make -C easel tests make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o easel_utest -I. -I. -L. -DeslEASEL_TESTDRIVE ./easel.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_alloc_utest -I. -I. -L. -DeslALLOC_TESTDRIVE ./esl_alloc.c -leasel -lm -lpthread ./easel.c: In function ‘esl_FileTail’: ./easel.c:1788:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1788 | lastslash = strrchr(path, eslDIRSLASH); | ^ ./easel.c: In function ‘esl_FileNewSuffix’: ./easel.c:1938:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1938 | lastdot = strrchr(filename, '.'); /* check for suffix to replace */ | ^ x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_alphabet_utest -I. -I. -L. -DeslALPHABET_TESTDRIVE ./esl_alphabet.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_bitfield_utest -I. -I. -L. -DeslBITFIELD_TESTDRIVE ./esl_bitfield.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_buffer_utest -I. -I. -L. -DeslBUFFER_TESTDRIVE ./esl_buffer.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_cluster_utest -I. -I. -L. -DeslCLUSTER_TESTDRIVE ./esl_cluster.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_cpu_utest -I. -I. -L. -DeslCPU_TESTDRIVE ./esl_cpu.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dirichlet_utest -I. -I. -L. -DeslDIRICHLET_TESTDRIVE ./esl_dirichlet.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_distance_utest -I. -I. -L. -DeslDISTANCE_TESTDRIVE ./esl_distance.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dmatrix_utest -I. -I. -L. -DeslDMATRIX_TESTDRIVE ./esl_dmatrix.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dsqdata_utest -I. -I. -L. -DeslDSQDATA_TESTDRIVE ./esl_dsqdata.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_exponential_utest -I. -I. -L. -DeslEXPONENTIAL_TESTDRIVE ./esl_exponential.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_fileparser_utest -I. -I. -L. -DeslFILEPARSER_TESTDRIVE ./esl_fileparser.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gamma_utest -I. -I. -L. -DeslGAMMA_TESTDRIVE ./esl_gamma.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gencode_utest -I. -I. -L. -DeslGENCODE_TESTDRIVE ./esl_gencode.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_getopts_utest -I. -I. -L. -DeslGETOPTS_TESTDRIVE ./esl_getopts.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_graph_utest -I. -I. -L. -DeslGRAPH_TESTDRIVE ./esl_graph.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gumbel_utest -I. -I. -L. -DeslGUMBEL_TESTDRIVE ./esl_gumbel.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_heap_utest -I. -I. -L. -DeslHEAP_TESTDRIVE ./esl_heap.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_histogram_utest -I. -I. -L. -DeslHISTOGRAM_TESTDRIVE ./esl_histogram.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_hmm_utest -I. -I. -L. -DeslHMM_TESTDRIVE ./esl_hmm.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_huffman_utest -I. -I. -L. -DeslHUFFMAN_TESTDRIVE ./esl_huffman.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_hyperexp_utest -I. -I. -L. -DeslHYPEREXP_TESTDRIVE ./esl_hyperexp.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_iset_utest -I. -I. -L. -DeslISET_TESTDRIVE ./esl_iset.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_json_utest -I. -I. -L. -DeslJSON_TESTDRIVE ./esl_json.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_keyhash_utest -I. -I. -L. -DeslKEYHASH_TESTDRIVE ./esl_keyhash.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_lognormal_utest -I. -I. -L. -DeslLOGNORMAL_TESTDRIVE ./esl_lognormal.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_matrixops_utest -I. -I. -L. -DeslMATRIXOPS_TESTDRIVE ./esl_matrixops.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_mem_utest -I. -I. -L. -DeslMEM_TESTDRIVE ./esl_mem.c -leasel -lm -lpthread ./esl_mem.c: In function ‘esl_memnewline’: ./esl_mem.c:486:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 486 | char *ptr = memchr(m, '\n', n); | ^~~~~~ x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_minimizer_utest -I. -I. -L. -DeslMINIMIZER_TESTDRIVE ./esl_minimizer.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_mixdchlet_utest -I. -I. -L. -DeslMIXDCHLET_TESTDRIVE ./esl_mixdchlet.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msa_utest -I. -I. -L. -DeslMSA_TESTDRIVE ./esl_msa.c -leasel -lm -lpthread ./esl_msa.c: In function ‘esl_msa_SymConvert’: ./esl_msa.c:2774:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2774 | if ((sptr = strchr(oldsyms, msa->aseq[idx][apos])) != NULL) | ^ x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msacluster_utest -I. -I. -L. -DeslMSACLUSTER_TESTDRIVE ./esl_msacluster.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_utest -I. -I. -L. -DeslMSAFILE_TESTDRIVE ./esl_msafile.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile2_utest -I. -I. -L. -DeslMSAFILE2_TESTDRIVE ./esl_msafile2.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_a2m_utest -I. -I. -L. -DeslMSAFILE_A2M_TESTDRIVE ./esl_msafile_a2m.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_afa_utest -I. -I. -L. -DeslMSAFILE_AFA_TESTDRIVE ./esl_msafile_afa.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_clustal_utest -I. -I. -L. -DeslMSAFILE_CLUSTAL_TESTDRIVE ./esl_msafile_clustal.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_phylip_utest -I. -I. -L. -DeslMSAFILE_PHYLIP_TESTDRIVE ./esl_msafile_phylip.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_psiblast_utest -I. -I. -L. -DeslMSAFILE_PSIBLAST_TESTDRIVE ./esl_msafile_psiblast.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_selex_utest -I. -I. -L. -DeslMSAFILE_SELEX_TESTDRIVE ./esl_msafile_selex.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_stockholm_utest -I. -I. -L. -DeslMSAFILE_STOCKHOLM_TESTDRIVE ./esl_msafile_stockholm.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msaweight_utest -I. -I. -L. -DeslMSAWEIGHT_TESTDRIVE ./esl_msaweight.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_normal_utest -I. -I. -L. -DeslNORMAL_TESTDRIVE ./esl_normal.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_quicksort_utest -I. -I. -L. -DeslQUICKSORT_TESTDRIVE ./esl_quicksort.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_random_utest -I. -I. -L. -DeslRANDOM_TESTDRIVE ./esl_random.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_rand64_utest -I. -I. -L. -DeslRAND64_TESTDRIVE ./esl_rand64.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_randomseq_utest -I. -I. -L. -DeslRANDOMSEQ_TESTDRIVE ./esl_randomseq.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_ratematrix_utest -I. -I. -L. -DeslRATEMATRIX_TESTDRIVE ./esl_ratematrix.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_red_black_utest -I. -I. -L. -DeslRED_BLACK_TESTDRIVE ./esl_red_black.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_recorder_utest -I. -I. -L. -DeslRECORDER_TESTDRIVE ./esl_recorder.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_regexp_utest -I. -I. -L. -DeslREGEXP_TESTDRIVE ./esl_regexp.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_rootfinder_utest -I. -I. -L. -DeslROOTFINDER_TESTDRIVE ./esl_rootfinder.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_scorematrix_utest -I. -I. -L. -DeslSCOREMATRIX_TESTDRIVE ./esl_scorematrix.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sq_utest -I. -I. -L. -DeslSQ_TESTDRIVE ./esl_sq.c -leasel -lm -lpthread ./esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ./esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:676:14: note: in a call to allocation function ‘malloc’ declared here 676 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sqio_utest -I. -I. -L. -DeslSQIO_TESTDRIVE ./esl_sqio.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_ssi_utest -I. -I. -L. -DeslSSI_TESTDRIVE ./esl_ssi.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stack_utest -I. -I. -L. -DeslSTACK_TESTDRIVE ./esl_stack.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stats_utest -I. -I. -L. -DeslSTATS_TESTDRIVE ./esl_stats.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stretchexp_utest -I. -I. -L. -DeslSTRETCHEXP_TESTDRIVE ./esl_stretchexp.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_tree_utest -I. -I. -L. -DeslTREE_TESTDRIVE ./esl_tree.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_varint_utest -I. -I. -L. -DeslVARINT_TESTDRIVE ./esl_varint.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_vectorops_utest -I. -I. -L. -DeslVECTOROPS_TESTDRIVE ./esl_vectorops.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_weibull_utest -I. -I. -L. -DeslWEIBULL_TESTDRIVE ./esl_weibull.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_wuss_utest -I. -I. -L. -DeslWUSS_TESTDRIVE ./esl_wuss.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sse_utest -I. -I. -L. -DeslSSE_TESTDRIVE ./esl_sse.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_avx_utest -I. -I. -L. -DeslAVX_TESTDRIVE ./esl_avx.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_avx512_utest -I. -I. -L. -DeslAVX512_TESTDRIVE ./esl_avx512.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_neon_utest -I. -I. -L. -DeslNEON_TESTDRIVE ./esl_neon.c -leasel -lm -lpthread x86_64-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_vmx_utest -I. -I. -L. -DeslVMX_TESTDRIVE ./esl_vmx.c -leasel -lm -lpthread /usr/bin/make -C miniapps tests make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[4]: Nothing to be done for 'tests'. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' /usr/bin/make -C src tests make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' /usr/bin/make -C impl_sse libhmmer-impl.stamp x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o itest_brute.o -c itest_brute.c make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[4]: 'libhmmer-impl.stamp' is up to date. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7BUILD_TESTDRIVE -o build_utest ./build.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_FWDBACK_TESTDRIVE -o generic_fwdback_utest ./generic_fwdback.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_FWDBACK_CHK_TESTDRIVE -o generic_fwdback_chk_utest ./generic_fwdback_chk.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_MSV_TESTDRIVE -o generic_msv_utest ./generic_msv.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_STOTRACE_TESTDRIVE -o generic_stotrace_utest ./generic_stotrace.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_VITERBI_TESTDRIVE -o generic_viterbi_utest ./generic_viterbi.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMER_TESTDRIVE -o hmmer_utest ./hmmer.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7LOGSUM_TESTDRIVE -o logsum_utest ./logsum.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7MODELCONFIG_TESTDRIVE -o modelconfig_utest ./modelconfig.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7SEQMODEL_TESTDRIVE -o seqmodel_utest ./seqmodel.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7ALIDISPLAY_TESTDRIVE -o p7_alidisplay_utest ./p7_alidisplay.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7BG_TESTDRIVE -o p7_bg_utest ./p7_bg.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7DOMAIN_TESTDRIVE -o p7_domain_utest ./p7_domain.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GMX_TESTDRIVE -o p7_gmx_utest ./p7_gmx.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GMXCHK_TESTDRIVE -o p7_gmxchk_utest ./p7_gmxchk.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HIT_TESTDRIVE -o p7_hit_utest ./p7_hit.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMD_SEARCH_STATS_TESTDRIVE -o p7_hmmd_search_stats_utest ./p7_hmmd_search_stats.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMM_TESTDRIVE -o p7_hmm_utest ./p7_hmm.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMFILE_TESTDRIVE -o p7_hmmfile_utest ./p7_hmmfile.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7PROFILE_TESTDRIVE -o p7_profile_utest ./p7_profile.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7TOPHITS_TESTDRIVE -o p7_tophits_utest ./p7_tophits.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7TRACE_TESTDRIVE -o p7_trace_utest ./p7_trace.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7SCOREDATA_TESTDRIVE -o p7_scoredata_utest ./p7_scoredata.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMPGMD2MSA_TESTDRIVE -o hmmpgmd2msa_utest ./hmmpgmd2msa.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMD_SEARCH_STATUS_TESTDRIVE -o hmmd_search_status_utest ./hmmd_search_status.c -lhmmer -leasel -ldivsufsort -lpthread -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o itest_brute itest_brute.o -lhmmer -leasel -ldivsufsort -lpthread -lm /usr/bin/make -C impl_sse tests make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7DECODING_TESTDRIVE -o decoding_utest ./decoding.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7FWDBACK_TESTDRIVE -o fwdback_utest ./fwdback.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7IO_TESTDRIVE -o io_utest ./io.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7MSVFILTER_TESTDRIVE -o msvfilter_utest ./msvfilter.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7NULL2_TESTDRIVE -o null2_utest ./null2.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7OPTACC_TESTDRIVE -o optacc_utest ./optacc.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7STOTRACE_TESTDRIVE -o stotrace_utest ./stotrace.c -lhmmer -leasel -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hmmer-2ml2gJ/hmmer-3.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7VITFILTER_TESTDRIVE -o vitfilter_utest ./vitfilter.c -lhmmer -leasel -lm make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' /usr/bin/make check -j 2 | tee debian/test_log make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' /usr/bin/make -C easel tests make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' /usr/bin/make -C miniapps tests make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[4]: Nothing to be done for 'tests'. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' /usr/bin/make -C src tests make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' /usr/bin/make -C impl_sse libhmmer-impl.stamp make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[4]: 'libhmmer-impl.stamp' is up to date. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' /usr/bin/make -C impl_sse tests make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[4]: Nothing to be done for 'tests'. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' /usr/bin/make -C easel check make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' /usr/bin/make -C miniapps check make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' /usr/bin/make -C testsuite check make[4]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/testsuite' Running Easel test suite... exercise 1 [ easel-utest] ... ok. exercise 2 [ alloc-utest] ... ok. exercise 3 [ alphabet-utest] ... ok. exercise 4 [ avx-utest] ... ok. exercise 5 [ avx512-utest] ... ok. exercise 6 [ bitfield-utest] ... ok. exercise 7 [ buffer-utest] ... ok. exercise 8 [ cluster-utest] ... ok. exercise 9 [ cpu-utest] ... ok. exercise 10 [ dirichlet-utest] ... ok. exercise 11 [ distance-utest] ... ok. exercise 12 [ dmatrix-utest] ... ok. exercise 13 [ dsqdata-utest] ... ok. exercise 14 [ exponential-utest] ... ok. exercise 15 [ fileparser-utest] ... ok. exercise 16 [ gamma-utest] ... ok. exercise 17 [ gencode-utest] ... ok. exercise 18 [ getopts-utest] ... ok. exercise 19 [ graph-utest] ... ok. exercise 20 [ gumbel-utest] ... ok. exercise 21 [ heap-utest] ... ok. exercise 22 [ histogram-utest] ... ok. exercise 23 [ huffman-utest] ... ok. exercise 24 [ hyperexp-utest] ... ok. exercise 25 [ iset-utest] ... ok. exercise 26 [ json-utest] ... ok. exercise 27 [ keyhash-utest] ... ok. exercise 28 [ lognormal-utest] ... ok. exercise 29 [ matrixops-utest] ... ok. exercise 30 [ mem-utest] ... ok. exercise 31 [ minimizer-utest] ... ok. exercise 32 [ mixdchlet-utest] ... ok. exercise 33 [ msa-utest] ... ok. exercise 34 [ msacluster-utest] ... ok. exercise 35 [ msafile] ... ok. exercise 36 [ msafile2] ... ok. exercise 37 [ msafile-a2m] ... ok. exercise 38 [ msafile-afa] ... ok. exercise 39 [ msafile-clustal] ... ok. exercise 40 [ msafile-phylip] ... ok. exercise 41 [ msafile-psiblast] ... ok. exercise 42 [ msafile-selex] ... ok. exercise 43 [ msafile-stockholm] ... ok. exercise 44 [ msaweight-utest] ... ok. exercise 45 [ neon-utest] ... ok. exercise 46 [ normal-utest] ... ok. exercise 47 [ quicksort-utest] ... ok. exercise 48 [ random-utest] ... ok. exercise 49 [ rand64-utest] ... ok. exercise 50 [ randomseq-utest] ... ok. exercise 51 [ ratematrix-utest] ... ok. exercise 52 [ recorder-utest] ... ok. exercise 53 [ red_black-utest] ... ok. exercise 54 [ regexp-utest] ... ok. exercise 55 [ rootfinder-utest] ... ok. exercise 56 [ scorematrix-utest] ... ok. exercise 57 [ sq-utest] ... ok. exercise 58 [ sqio-utest] ... ok. exercise 59 [ sse-utest] ... ok. exercise 60 [ ssi-utest] ... ok. exercise 61 [ stack-utest] ... ok. exercise 62 [ stats-utest] ... ok. exercise 63 [ stretchexp-utest] ... ok. exercise 64 [ tree-utest] ... ok. exercise 65 [ varint-utest] ... ok. exercise 66 [ vectorops-utest] ... ok. exercise 67 [ vmx-utest] ... ok. exercise 68 [ weibull-utest] ... ok. exercise 69 [ wuss-utest] ... ok. exercise 70 [ e2] ... ok. exercise 71 [ degen-residues] ... ok. exercise 72 [ ncbi-indices] ... ok. exercise 73 [ blank-gf] ... ok. exercise 74 [ sindi] ... ok. exercise 75 [ esl-translate] ... ok. exercise 76 [ esl-afetch] ... ok. exercise 77 [ esl-alimanip] ... ok. exercise 78 [ esl-alimap] ... ok. exercise 79 [ esl-alimask] ... ok. exercise 80 [ esl-alimerge] ... ok. exercise 81 [ esl-alistat] ... ok. exercise 82 [ esl-compalign] ... ok. exercise 83 [ esl-construct] ... ok. exercise 84 [ esl-mask] ... ok. exercise 85 [ esl-seqrange] ... ok. exercise 86 [ esl-shuffle] ... ok. exercise 87 [ esl-ssdraw] ... ok. All 87 exercises at level <= 2 passed. System information: Sun Sep 20 00:02:13 UTC 2026 Linux carme 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) x86_64 GNU/Linux make[4]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/testsuite' make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' /usr/bin/make -C testsuite check make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/testsuite' Running HMMER test suite... exercise 1 [ hmmer] ... ok. exercise 2 [ build] ... ok. exercise 3 [ generic_fwdback] ... ok. exercise 4 [ generic_msv] ... ok. exercise 5 [ generic_stotrace] ... ok. exercise 6 [ generic_viterbi] ... ok. exercise 7 [ hmmd_search_status] ... ok. exercise 8 [ logsum] ... ok. exercise 9 [ modelconfig] ... ok. exercise 10 [ seqmodel] ... ok. exercise 11 [ p7_alidisplay] ... ok. exercise 12 [ p7_bg] ... ok. exercise 13 [ p7_domain] ... ok. exercise 14 [ p7_gmx] ... ok. exercise 15 [ p7_hit] ... ok. exercise 16 [ p7_hmm] ... ok. exercise 17 [ p7_hmmfile] ... ok. exercise 18 [ p7_hmmd_search_stats] ... ok. exercise 19 [ p7_profile] ... ok. exercise 20 [ p7_tophits] ... ok. exercise 21 [ p7_trace] ... ok. exercise 22 [ p7_scoredata] ... ok. exercise 23 [ decoding] ... ok. exercise 24 [ fwdback] ... ok. exercise 25 [ io] ... ok. exercise 26 [ msvfilter] ... ok. exercise 27 [ null2] ... ok. exercise 28 [ optacc] ... ok. exercise 29 [ stotrace] ... ok. exercise 30 [ vitfilter] ... ok. exercise 31 [ hmmpgmd2msa] ... ok. exercise 32 [ hmmalign] ... ok. exercise 33 [ hmmalign/-h] ... ok. exercise 34 [ hmmalign/-o] ... ok. exercise 35 [ hmmalign/--mapali] ... ok. exercise 36 [ hmmalign/--trim] ... ok. exercise 37 [ hmmalign/--amino] ... ok. exercise 38 [ hmmalign/--informat] ... ok. exercise 39 [ hmmalign/--outformat] ... ok. exercise 40 [ hmmbuild] ... ok. exercise 41 [ build/-h] ... ok. exercise 42 [ build/-n] ... ok. exercise 43 [ build/-o] ... ok. exercise 44 [ build/-O] ... ok. exercise 45 [ build/--amino] ... ok. exercise 46 [ build/--dna] ... ok. exercise 47 [ build/--rna] ... ok. exercise 48 [ build/--fast] ... ok. exercise 49 [ build/--hand] ... ok. exercise 50 [ build/--symfrac] ... ok. exercise 51 [ build/--fragthresh] ... ok. exercise 52 [ build/--wpb] ... ok. exercise 53 [ build/--wgsc] ... ok. exercise 54 [ build/--wblosum] ... ok. exercise 55 [ build/--wnone] ... ok. exercise 56 [ build/--wid] ... ok. exercise 57 [ build/--eent] ... ok. exercise 58 [ build/--eclust] ... ok. exercise 59 [ build/--enone] ... ok. exercise 60 [ build/--eset] ... ok. exercise 61 [ build/--ere] ... ok. exercise 62 [ build/--esigma] ... ok. exercise 63 [ build/--eid] ... ok. exercise 64 [ build/--pnone] ... ok. exercise 65 [ build/--plaplace] ... ok. exercise 66 [ build/--EmL] ... ok. exercise 67 [ build/--EmN] ... ok. exercise 68 [ build/--EvL] ... ok. exercise 69 [ build/--EvN] ... ok. exercise 70 [ build/--EfL] ... ok. exercise 71 [ build/--EfN] ... ok. exercise 72 [ build/--Eft] ... ok. exercise 73 [ build/--informat] ... ok. exercise 74 [ build/--seed] ... ok. exercise 75 [ search] ... ok. exercise 76 [ search/-h] ... ok. exercise 77 [ search/-o] ... ok. exercise 78 [ search/-A] ... ok. exercise 79 [ search/--tblout] ... ok. exercise 80 [ search/--domtblout] ... ok. exercise 81 [ search/--pfamtblout] ... ok. exercise 82 [ search/--acc] ... ok. exercise 83 [ search/--noali] ... ok. exercise 84 [ search/--notextw] ... ok. exercise 85 [ search/--textw] ... ok. exercise 86 [ search/-E] ... ok. exercise 87 [ search/-T] ... ok. exercise 88 [ search/--domE] ... ok. exercise 89 [ search/--domT] ... ok. exercise 90 [ search/--incE] ... ok. exercise 91 [ search/--incT] ... ok. exercise 92 [ search/--incdomE] ... ok. exercise 93 [ search/--incdomT] ... ok. exercise 94 [ search/--cut_ga] ... ok. exercise 95 [ search/--cut_nc] ... ok. exercise 96 [ search/--cut_tc] ... ok. exercise 97 [ search/--max] ... ok. exercise 98 [ search/--F1] ... ok. exercise 99 [ search/--F2] ... ok. exercise 100 [ search/--F3] ... ok. exercise 101 [ search/--nobias] ... ok. exercise 102 [ search/--nonull2] ... ok. exercise 103 [ search/-Z] ... ok. exercise 104 [ search/--domZ] ... ok. exercise 105 [ search/--seed] ... ok. exercise 106 [ search/--tformat] ... ok. exercise 107 [ hmmscan] ... ok. exercise 108 [ scan/-h] ... ok. exercise 109 [ scan/-o] ... ok. exercise 110 [ scan/--tblout] ... ok. exercise 111 [ scan/--domtblout] ... ok. exercise 112 [ scan/--pfamtblout] ... ok. exercise 113 [ scan/--acc] ... ok. exercise 114 [ scan/--noali] ... ok. exercise 115 [ scan/--notextw] ... ok. exercise 116 [ scan/--textw] ... ok. exercise 117 [ scan/-E] ... ok. exercise 118 [ scan/-T] ... ok. exercise 119 [ scan/--domE] ... ok. exercise 120 [ scan/--domT] ... ok. exercise 121 [ scan/--incE] ... ok. exercise 122 [ scan/--incT] ... ok. exercise 123 [ scan/--incdomE] ... ok. exercise 124 [ scan/--incdomT] ... ok. exercise 125 [ scan/--incdomT] ... ok. exercise 126 [ scan/--cut_ga] ... ok. exercise 127 [ scan/--cut_nc] ... ok. exercise 128 [ scan/--cut_tc] ... ok. exercise 129 [ scan/--max] ... ok. exercise 130 [ scan/--F1] ... ok. exercise 131 [ scan/--F2] ... ok. exercise 132 [ scan/--F3] ... ok. exercise 133 [ scan/--nobias] ... ok. exercise 134 [ scan/--nonull2] ... ok. exercise 135 [ scan/-Z] ... ok. exercise 136 [ scan/--domZ] ... ok. exercise 137 [ scan/--seed] ... ok. exercise 138 [ scan/--qformat] ... ok. exercise 139 [ scan/--cpu] ... ok. exercise 140 [ jackhmmer] ... ok. exercise 141 [ j/-h] ... ok. exercise 142 [ j/-N] ... ok. exercise 143 [ j/-o] ... ok. exercise 144 [ j/-A] ... ok. exercise 145 [ j/--tblout] ... ok. exercise 146 [ j/--domtblout] ... ok. exercise 147 [ j/--chkhmm] ... ok. exercise 148 [ j/--chkali] ... ok. exercise 149 [ j/--acc] ... ok. exercise 150 [ j/--noali] ... ok. exercise 151 [ j/--notextw] ... ok. exercise 152 [ j/--textw] ... ok. exercise 153 [ j/--popen] ... ok. exercise 154 [ j/--pextend] ... ok. exercise 155 [ j/--mxfile] ... ok. exercise 156 [ j/-E] ... ok. exercise 157 [ j/-T] ... ok. exercise 158 [ j/--domE] ... ok. exercise 159 [ j/--domT] ... ok. exercise 160 [ j/--incE] ... ok. exercise 161 [ j/--incT] ... ok. exercise 162 [ j/--incdomE] ... ok. exercise 163 [ j/--incdomT] ... ok. exercise 164 [ j/--max] ... ok. exercise 165 [ j/--F1] ... ok. exercise 166 [ j/--F2] ... ok. exercise 167 [ j/--F3] ... ok. exercise 168 [ j/--nobias] ... ok. exercise 169 [ j/--EmL] ... ok. exercise 170 [ j/--EmN] ... ok. exercise 171 [ j/--EvL] ... ok. exercise 172 [ j/--EvN] ... ok. exercise 173 [ j/--EfL] ... ok. exercise 174 [ j/--EfN] ... ok. exercise 175 [ j/--Eft] ... ok. exercise 176 [ j/--nonull2] ... ok. exercise 177 [ j/-Z] ... ok. exercise 178 [ j/--domZ] ... ok. exercise 179 [ j/--seed] ... ok. exercise 180 [ j/--qformat] ... ok. exercise 181 [ j/--tformat] ... ok. exercise 182 [ phmmer] ... ok. exercise 183 [ phmmer/-h] ... ok. exercise 184 [ phmmer/-o] ... ok. exercise 185 [ phmmer/-A] ... ok. exercise 186 [ phmmer/--tblout] ... ok. exercise 187 [ phmmer/--domtblout] ... ok. exercise 188 [ phmmer/--pfamtblout] ... ok. exercise 189 [ phmmer/--acc] ... ok. exercise 190 [ phmmer/--noali] ... ok. exercise 191 [ phmmer/--notextw] ... ok. exercise 192 [ phmmer/--textw] ... ok. exercise 193 [ phmmer/--popen] ... ok. exercise 194 [ phmmer/--pextend] ... ok. exercise 195 [ phmmer/--mxfile] ... ok. exercise 196 [ phmmer/-E] ... ok. exercise 197 [ phmmer/-T] ... ok. exercise 198 [ phmmer/--domE] ... ok. exercise 199 [ phmmer/--domT] ... ok. exercise 200 [ phmmer/--incE] ... ok. exercise 201 [ phmmer/--incT] ... ok. exercise 202 [ phmmer/--incdomE] ... ok. exercise 203 [ phmmer/--incdomT] ... ok. exercise 204 [ phmmer/--max] ... ok. exercise 205 [ phmmer/--F1] ... ok. exercise 206 [ phmmer/--F2] ... ok. exercise 207 [ phmmer/--F3] ... ok. exercise 208 [ phmmer/--nobias] ... ok. exercise 209 [ phmmer/--EmL] ... ok. exercise 210 [ phmmer/--EmN] ... ok. exercise 211 [ phmmer/--EvL] ... ok. exercise 212 [ phmmer/--EvN] ... ok. exercise 213 [ phmmer/--EfL] ... ok. exercise 214 [ phmmer/--EfN] ... ok. exercise 215 [ phmmer/--Eft] ... ok. exercise 216 [ phmmer/--nonull2] ... ok. exercise 217 [ phmmer/-Z] ... ok. exercise 218 [ phmmer/--domZ] ... ok. exercise 219 [ phmmer/--seed] ... ok. exercise 220 [ phmmer/--qformat] ... ok. exercise 221 [ phmmer/--tformat] ... ok. exercise 222 [ nhmmer] ... ok. exercise 223 [ nhmmer/-h] ... ok. exercise 224 [ nhmmer/-o] ... ok. exercise 225 [ nhmmer/-A] ... ok. exercise 226 [ nhmmer/--tblout] ... ok. exercise 227 [ nhmmer/--dfamtblout] ... ok. exercise 228 [ nhmmer/--acc] ... ok. exercise 229 [ nhmmer/--noali] ... ok. exercise 230 [ nhmmer/--notextw] ... ok. exercise 231 [ nhmmer/--textw] ... ok. exercise 232 [ nhmmer/-E] ... ok. exercise 233 [ nhmmer/-T] ... ok. exercise 234 [ nhmmer/--incE] ... ok. exercise 235 [ nhmmer/--incT] ... ok. exercise 236 [ nhmmer/--max] ... ok. exercise 237 [ nhmmer/--F1] ... ok. exercise 238 [ nhmmer/--F2] ... ok. exercise 239 [ nhmmer/--F3] ... ok. exercise 240 [ nhmmer/--nobias] ... ok. exercise 241 [ nhmmer/--nonull2] ... ok. exercise 242 [ nhmmer/-Z] ... ok. exercise 243 [ nhmmer/--seed] ... ok. exercise 244 [ nhmmscan] ... ok. exercise 245 [ nhmmscan/-h] ... ok. exercise 246 [ nhmmscan/-o] ... ok. exercise 247 [ nhmmscan/--tblout] ... ok. exercise 248 [nhmmscan/--dfamtblout] ... ok. exercise 249 [ nhmmscan/--acc] ... ok. exercise 250 [ nhmmscan/--noali] ... ok. exercise 251 [ nhmmscan/--notextw] ... ok. exercise 252 [ nhmmscan/--textw] ... ok. exercise 253 [ nhmmscan/-E] ... ok. exercise 254 [ nhmmscan/-T] ... ok. exercise 255 [ nhmmscan/--incE] ... ok. exercise 256 [ nhmmscan/--incT] ... ok. exercise 257 [ nhmmscan/--max] ... ok. exercise 258 [ nhmmscan/--F1] ... ok. exercise 259 [ nhmmscan/--F2] ... ok. exercise 260 [ nhmmscan/--F3] ... ok. exercise 261 [ nhmmscan/--nobias] ... ok. exercise 262 [ nhmmscan/--nonull2] ... ok. exercise 263 [ nhmmscan/-Z] ... ok. exercise 264 [ nhmmscan/--seed] ... ok. exercise 265 [ hmmemit] ... ok. exercise 266 [ hmmemit/-h] ... ok. exercise 267 [ hmmemit/-c] ... ok. exercise 268 [ hmmemit/-o] ... ok. exercise 269 [ hmmemit/-p] ... ok. exercise 270 [ hmmemit/-N] ... ok. exercise 271 [ hmmemit/-L] ... ok. exercise 272 [ hmmemit/--local] ... ok. exercise 273 [ hmmemit/--unilocal] ... ok. exercise 274 [ hmmemit/--glocal] ... ok. exercise 275 [ hmmemit/--uniglocal] ... ok. exercise 276 [ hmmfetch] ... ok. exercise 277 [ hmmstat] ... ok. exercise 278 [ hmmlogo] ... ok. exercise 279 [ hmmconvert] ... ok. exercise 280 [ hmmsim] ... ok. exercise 281 [ hmmbuild_variation] ... ok. exercise 282 [ hmmscan_variation] ... ok. exercise 283 [ hmmsearch_variation] ... ok. exercise 284 [ phmmer_variation] ... ok. exercise 285 [ mapali] ... ok. exercise 286 [ fragments] ... ok. exercise 287 [ nonresidues] ... ok. exercise 288 [ opt-annotation] ... ok. exercise 289 [ dup-names] ... ok. exercise 290 [ mapali-again] ... ok. exercise 291 [ delete-corruption] ... ok. exercise 292 [ msa-integrity] ... ok. exercise 293 [ hmmemit-consensus] ... ok. exercise 294 [ hmmconvert] ... ok. exercise 295 [ stdin_pipes] ... ok. exercise 296 [ nhmmer_generic] ... ok. exercise 297 [ hmmpgmd_ga] ... ok. exercise 298 [ rewind] ... ok. exercise 299 [ hmmpgmd_shard_ga] ... ok. exercise 300 [ bad-fasta] ... ok. exercise 301 [ brute-itest] ... ok. exercise 302 [ hmmpress-itest] ... ok. exercise 303 [ h39] ... ok. exercise 304 [ h45] ... ok. exercise 305 [ h50] ... ok. exercise 306 [ h82] ... ok. exercise 307 [ iss159] ... ok. All 307 exercises at level <= 2 passed. System information: Sun Sep 20 00:02:29 UTC 2026 Linux carme 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) x86_64 GNU/Linux make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/testsuite' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' if tail -n 6 debian/test_log | head -n 1 | grep -q FAILED ; then false ; fi make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j2 install DESTDIR=/build/hmmer-2ml2gJ/hmmer-3.4\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' make -C easel all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' make -C miniapps all make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel/miniapps' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/easel' make -C src all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' make -C impl_sse libhmmer-impl.stamp make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[3]: 'libhmmer-impl.stamp' is up to date. make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src/impl_sse' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' make -C profmark all make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/profmark' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/profmark' if [ ! -d /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/bin ]; then /usr/bin/install -c -d /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/bin; fi if [ ! -d /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/share/man/man1 ]; then /usr/bin/install -c -d /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/share/man/man1; fi make -C src install make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \ /usr/bin/install -c -m 0755 $file /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/bin/ ;\ done make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/src' make -C documentation install make[2]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/documentation' make -C man install make[3]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/documentation/man' for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0664 $file.man /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/tmp/usr/share/man/man1/${file}.1 ;\ done make[3]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/documentation/man' make[2]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg/documentation' make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' mkdir -p /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/ cp src/hmmc2 /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/ make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' mkdir -p /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl find src/ -maxdepth 1 -name "*_utest" -exec cp \{\} /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/ \; find src/impl_sse -name "*_utest" -exec cp \{\} /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl \; cp src/itest_brute /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src cp src/hmmpress.itest.pl /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src cp -aR testsuite /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples find easel -name "*.o" -delete cp -aR easel /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples cp -aR tutorial /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples find /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name 'Makefile' | xargs sed -i "s^/build/hmmer-2ml2gJ/hmmer-3.4+dfsg^.^g" find /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name "esltmp*" -delete make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_compress -Xtutorial/ make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_fixperms debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' find debian -name .dropbox.attr -delete find debian -name "*.fa" -executable -exec chmod -x \{\} \; find /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name "*.man" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/hmmer-2ml2gJ/hmmer-3.4+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hmmer' in '../hmmer_3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'hmmer-doc' in '../hmmer-doc_3.4+dfsg-3_all.deb'. dpkg-deb: building package 'hmmer-examples' in '../hmmer-examples_3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'hmmer-dbgsym' in '../hmmer-dbgsym_3.4+dfsg-3_amd64.deb'. dpkg-genbuildinfo -O../hmmer_3.4+dfsg-3_amd64.buildinfo dpkg-genchanges -O../hmmer_3.4+dfsg-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from /build/hmmer-2ml2gJ/hmmer-3.4+dfsg/debian/source/options: --extend-diff-ignore=(^|/)config.(sub|guess)$ dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-09-20T00:03:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 20 Sep 2026 00:03:37 +0000 | +------------------------------------------------------------------------------+ hmmer_3.4+dfsg-3_amd64.changes: ------------------------------- Format: 1.8 Date: Mon, 29 Sep 2025 14:45:00 +0200 Source: hmmer Binary: hmmer hmmer-dbgsym hmmer-doc hmmer-examples Architecture: source amd64 all Version: 3.4+dfsg-3 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila Description: hmmer - profile hidden Markov models for protein sequence analysis hmmer-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer-examples - profile hidden Markov models for protein sequence analysis (examp Closes: 1103312 Changes: hmmer (3.4+dfsg-3) unstable; urgency=medium . * Team upload. . [ Michael R. Crusoe ] * d/rules: use DEB_BUILD_OPTION_PARALLEL instead of nproc to respect Debian Policy 4.9.1. . [ Santiago Vila ] * d/rules: Put V=VERBOSE at the beginning to be used in all targets. * d/rules: Do not filter nocheck in override_dh_auto_test, dh already does that. * d/rules: make tests after dh_auto_build, required by dh_installexamples. Fixes FTBFS when built with nocheck build profile. Closes: #1103312. * d/rules: Use execute_after_* where possible. * d/salsa-ci.yml: Use the simplified form. * d/salsa-ci.yml: Disable reprotest job, it does not work. * d/salsa-ci.yml: Enable nocheck build profile job. * d/control: Drop "Rules-Required-Root: no", no longer needed. * d/control: Update standards-version. Checksums-Sha1: 60dfaa8030704512c19b364d449e356ea1fee47a 1236 hmmer_3.4+dfsg-3.dsc 6cd56859757f272d77bccac774f464bbf306ef36 12996 hmmer_3.4+dfsg-3.debian.tar.xz 0256c964d298db75995fe17436f9e14cd90061c2 12941456 hmmer-dbgsym_3.4+dfsg-3_amd64.deb 3b2dfe63775f85a1e951bdd3c26a2e9accef600f 772484 hmmer-doc_3.4+dfsg-3_all.deb e51b77c8326aebc846e9178026765e7ed8e7fe23 32825788 hmmer-examples_3.4+dfsg-3_amd64.deb aced8155c2a2ad3ca2994413d2b59830a190324c 6241 hmmer_3.4+dfsg-3_amd64.buildinfo b996f74812e61c68b7287e1e489a61368cceef0a 1096056 hmmer_3.4+dfsg-3_amd64.deb Checksums-Sha256: 51294b11a16001b3bbd0cde02b74d4b53811039669dcab66e2fd525094b49abc 1236 hmmer_3.4+dfsg-3.dsc 778558b4904a9504be24d008c7442fac55077110fbfa7b834cc74aa68410967d 12996 hmmer_3.4+dfsg-3.debian.tar.xz 17ee4014e9500922c4e2f298fb3805bdcb98d0fd9b592646e573e150c9da7aea 12941456 hmmer-dbgsym_3.4+dfsg-3_amd64.deb e6147abf4e4844b1821f6cf2b13d9fdc6fc1295bc02ae1cd4ad0bfbd471b0150 772484 hmmer-doc_3.4+dfsg-3_all.deb c13c9d89e8d3213cb1700747a12c0cd625761847e76f9176c1579271c83078e0 32825788 hmmer-examples_3.4+dfsg-3_amd64.deb d522d9f2627986f10ff89195a6f7bcdb1ca6d6997a1cedd66218959ede258213 6241 hmmer_3.4+dfsg-3_amd64.buildinfo e4315462c1958aefc3ed4c5b395e311499398de4db5722d271b69dbc76f9eb0b 1096056 hmmer_3.4+dfsg-3_amd64.deb Files: 3de212b8b7ac1e979554d6289b187697 1236 science optional hmmer_3.4+dfsg-3.dsc 4a22660367a959d958af905a7dd7fa1e 12996 science optional hmmer_3.4+dfsg-3.debian.tar.xz 39cdeeae6f9a9655e7ebf6cf697fc76c 12941456 debug optional hmmer-dbgsym_3.4+dfsg-3_amd64.deb b7c0afbe1942cdd98ad49e2dcbdcebfc 772484 doc optional hmmer-doc_3.4+dfsg-3_all.deb b2d6015afff54139ef4d209f0691e322 32825788 doc optional hmmer-examples_3.4+dfsg-3_amd64.deb 2948e5da53d9e09357b78ecff03d120a 6241 science optional hmmer_3.4+dfsg-3_amd64.buildinfo 0fcad00094b423647ba775d48bd1f22c 1096056 science optional hmmer_3.4+dfsg-3_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 20 Sep 2026 00:03:37 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: hmmer Binary: hmmer hmmer-dbgsym hmmer-doc hmmer-examples Architecture: all amd64 source Version: 3.4+dfsg-3 Checksums-Md5: 3de212b8b7ac1e979554d6289b187697 1236 hmmer_3.4+dfsg-3.dsc 39cdeeae6f9a9655e7ebf6cf697fc76c 12941456 hmmer-dbgsym_3.4+dfsg-3_amd64.deb b7c0afbe1942cdd98ad49e2dcbdcebfc 772484 hmmer-doc_3.4+dfsg-3_all.deb b2d6015afff54139ef4d209f0691e322 32825788 hmmer-examples_3.4+dfsg-3_amd64.deb 0fcad00094b423647ba775d48bd1f22c 1096056 hmmer_3.4+dfsg-3_amd64.deb Checksums-Sha1: 60dfaa8030704512c19b364d449e356ea1fee47a 1236 hmmer_3.4+dfsg-3.dsc 0256c964d298db75995fe17436f9e14cd90061c2 12941456 hmmer-dbgsym_3.4+dfsg-3_amd64.deb 3b2dfe63775f85a1e951bdd3c26a2e9accef600f 772484 hmmer-doc_3.4+dfsg-3_all.deb e51b77c8326aebc846e9178026765e7ed8e7fe23 32825788 hmmer-examples_3.4+dfsg-3_amd64.deb b996f74812e61c68b7287e1e489a61368cceef0a 1096056 hmmer_3.4+dfsg-3_amd64.deb Checksums-Sha256: 51294b11a16001b3bbd0cde02b74d4b53811039669dcab66e2fd525094b49abc 1236 hmmer_3.4+dfsg-3.dsc 17ee4014e9500922c4e2f298fb3805bdcb98d0fd9b592646e573e150c9da7aea 12941456 hmmer-dbgsym_3.4+dfsg-3_amd64.deb e6147abf4e4844b1821f6cf2b13d9fdc6fc1295bc02ae1cd4ad0bfbd471b0150 772484 hmmer-doc_3.4+dfsg-3_all.deb c13c9d89e8d3213cb1700747a12c0cd625761847e76f9176c1579271c83078e0 32825788 hmmer-examples_3.4+dfsg-3_amd64.deb e4315462c1958aefc3ed4c5b395e311499398de4db5722d271b69dbc76f9eb0b 1096056 hmmer_3.4+dfsg-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 20 Sep 2026 00:03:36 +0000 Build-Path: /build/hmmer-2ml2gJ/hmmer-3.4+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-4), binutils (= 2.47-6), binutils-common (= 2.47-6), binutils-x86-64-linux-gnu (= 2.47-6), bsdextrautils (= 2.42.3-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-15 (= 15.3.0-4), cpp-15-x86-64-linux-gnu (= 15.3.0-4), cpp-16 (= 16.2.0-3), cpp-16-x86-64-linux-gnu (= 16.2.0-3), cpp-x86-64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.11.0-2), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-x86-64-linux-gnu (= 16.2.0-3), g++-x86-64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-15 (= 15.3.0-4), gcc-15-base (= 15.3.0-4), gcc-15-x86-64-linux-gnu (= 15.3.0-4), gcc-16 (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-16-x86-64-linux-gnu (= 16.2.0-3), gcc-x86-64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.14-1), hostname (= 3.25), init-system-helpers (= 1.69+nmu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b2), libbinutils (= 2.47-6), libblkid1 (= 2.42.3-1), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.43-5), libc-dev-bin (= 2.43-5), libc-gconv-modules-extra (= 2.43-5), libc6 (= 2.43-5), libc6-dev (= 2.43-5), libcap-ng0 (= 0.9.6-1), libcc1-0 (= 16.2.0-3), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdivsufsort-dev (= 2.0.1-7+b1), libdivsufsort3 (= 2.0.1-7+b1), libdpkg-perl (= 1.23.11), libelf1t64 (= 0.196-1), libexpat1 (= 2.8.4-1), libffi8 (= 3.8.0-2), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-4), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libhwasan0 (= 16.2.0-3), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), liblsan0 (= 16.2.0-3), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.3-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncursesw6 (= 6.6+20260608-2), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.48-3), libperl5.44 (= 5.44.0-1), libpipeline1 (= 1.5.8-3), libpython3-stdlib (= 3.14.7-3), libpython3.14-minimal (= 3.14.7-4), libpython3.14-stdlib (= 3.14.7-4), libquadmath0 (= 16.2.0-3), libreadline8t64 (= 8.3-4), libseccomp2 (= 2.6.1-1+b1), libselinux1 (= 3.11-2), libsframe3 (= 2.47-6), libsmartcols1 (= 2.42.3-1), libsqlite3-0 (= 3.53.4-2), libssl3t64 (= 3.6.4-1), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd0 (= 262~rc3-1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 262~rc3-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.3-1), libxml2-16 (= 2.15.4+dfsg-1), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.6-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), netbase (= 6.6), openssl-provider-legacy (= 3.6.4-1), patch (= 2.8-2), perl (= 5.44.0-1), perl-base (= 5.44.0-1), perl-modules-5.44 (= 5.44.0-1), po-debconf (= 1.0.22), python3 (= 3.14.7-3), python3-minimal (= 3.14.7-3), python3.14 (= 3.14.7-4), python3.14-minimal (= 3.14.7-4), readline-common (= 8.3-4), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-6), tzdata (= 2026c-1), util-linux (= 2.42.3-1), xz-utils (= 5.8.4-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1759149900" +------------------------------------------------------------------------------+ | Package contents Sun, 20 Sep 2026 00:03:37 +0000 | +------------------------------------------------------------------------------+ hmmer-dbgsym_3.4+dfsg-3_amd64.deb --------------------------------- new Debian package, version 2.0. size 12941456 bytes: control archive=1516 bytes. 1149 bytes, 12 lines control 2202 bytes, 21 lines md5sums Package: hmmer-dbgsym Source: hmmer Version: 3.4+dfsg-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 14035 Depends: hmmer (= 3.4+dfsg-3) Section: debug Priority: optional Description: debug symbols for hmmer Build-Ids: 0ac0ed8f15c732476e96a6bbea74d1ce3887f09e 0aee1b968460eb7910d514281061d5698a1ca009 1d930df0252191df49a8b085dd532a325e64282d 28bf3c3f86ad29dbffddb7a9a578deb2f3317f1b 41dea9a78f61b56003cde641faaf4be25af00339 43a98af76bdfc76fdb9836ab3223fd292eec6147 4d118158b4c33ab10be63dd57e3501dfee565f70 4f2e9c9391ae23b438c49a880e988cc21996500b 509153ba4c04ffb1342d47b9ab809762e4f90d7a 5bffcc100aaec2c421743eb3199801ec773ebe11 6560f0756d2ca7bb3e95173471d50ec8260730e7 8746833f5ccd44ede22f81c6a8b410867a17e636 87ce47b9c0ea81328aebc78a25adb141bbd6a478 a7029ce6266d478df46b28ea07a0961810b3a710 aa31bbdae018d68d7ba616408833ff85bc2d86cc b868f4d4453391738e048554a46d40f14e0f467d bf34b28ea4e4f730749efedc1dfb441aa3f43cfa d47f1e406d3bd950634f72775063e94bcd3441b3 e30dff9bfd23279f0ea3c872f9c3f611acfb536c fca82b1054d1ddc7f34191feb8adfe4ce2f70fac drwxr-xr-x root/root 0 2025-09-29 12:45 ./ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/0a/ -rw-r--r-- root/root 172424 2025-09-29 12:45 ./usr/lib/debug/.build-id/0a/c0ed8f15c732476e96a6bbea74d1ce3887f09e.debug -rw-r--r-- root/root 939016 2025-09-29 12:45 ./usr/lib/debug/.build-id/0a/ee1b968460eb7910d514281061d5698a1ca009.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/1d/ -rw-r--r-- root/root 547576 2025-09-29 12:45 ./usr/lib/debug/.build-id/1d/930df0252191df49a8b085dd532a325e64282d.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/28/ -rw-r--r-- root/root 534952 2025-09-29 12:45 ./usr/lib/debug/.build-id/28/bf3c3f86ad29dbffddb7a9a578deb2f3317f1b.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/41/ -rw-r--r-- root/root 318696 2025-09-29 12:45 ./usr/lib/debug/.build-id/41/dea9a78f61b56003cde641faaf4be25af00339.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/43/ -rw-r--r-- root/root 1137056 2025-09-29 12:45 ./usr/lib/debug/.build-id/43/a98af76bdfc76fdb9836ab3223fd292eec6147.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/4d/ -rw-r--r-- root/root 838008 2025-09-29 12:45 ./usr/lib/debug/.build-id/4d/118158b4c33ab10be63dd57e3501dfee565f70.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/4f/ -rw-r--r-- root/root 523144 2025-09-29 12:45 ./usr/lib/debug/.build-id/4f/2e9c9391ae23b438c49a880e988cc21996500b.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/50/ -rw-r--r-- root/root 942792 2025-09-29 12:45 ./usr/lib/debug/.build-id/50/9153ba4c04ffb1342d47b9ab809762e4f90d7a.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/5b/ -rw-r--r-- root/root 945448 2025-09-29 12:45 ./usr/lib/debug/.build-id/5b/ffcc100aaec2c421743eb3199801ec773ebe11.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/65/ -rw-r--r-- root/root 787280 2025-09-29 12:45 ./usr/lib/debug/.build-id/65/60f0756d2ca7bb3e95173471d50ec8260730e7.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/87/ -rw-r--r-- root/root 1018136 2025-09-29 12:45 ./usr/lib/debug/.build-id/87/46833f5ccd44ede22f81c6a8b410867a17e636.debug -rw-r--r-- root/root 1013432 2025-09-29 12:45 ./usr/lib/debug/.build-id/87/ce47b9c0ea81328aebc78a25adb141bbd6a478.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/a7/ -rw-r--r-- root/root 555568 2025-09-29 12:45 ./usr/lib/debug/.build-id/a7/029ce6266d478df46b28ea07a0961810b3a710.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/aa/ -rw-r--r-- root/root 568048 2025-09-29 12:45 ./usr/lib/debug/.build-id/aa/31bbdae018d68d7ba616408833ff85bc2d86cc.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/b8/ -rw-r--r-- root/root 1020144 2025-09-29 12:45 ./usr/lib/debug/.build-id/b8/68f4d4453391738e048554a46d40f14e0f467d.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/bf/ -rw-r--r-- root/root 269296 2025-09-29 12:45 ./usr/lib/debug/.build-id/bf/34b28ea4e4f730749efedc1dfb441aa3f43cfa.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/d4/ -rw-r--r-- root/root 521720 2025-09-29 12:45 ./usr/lib/debug/.build-id/d4/7f1e406d3bd950634f72775063e94bcd3441b3.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/e3/ -rw-r--r-- root/root 910856 2025-09-29 12:45 ./usr/lib/debug/.build-id/e3/0dff9bfd23279f0ea3c872f9c3f611acfb536c.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.build-id/fc/ -rw-r--r-- root/root 611368 2025-09-29 12:45 ./usr/lib/debug/.build-id/fc/a82b1054d1ddc7f34191feb8adfe4ce2f70fac.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 155656 2025-09-29 12:45 ./usr/lib/debug/.dwz/x86_64-linux-gnu/hmmer.debug drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer-dbgsym -> hmmer hmmer-doc_3.4+dfsg-3_all.deb ---------------------------- new Debian package, version 2.0. size 772484 bytes: control archive=1244 bytes. 890 bytes, 22 lines control 1177 bytes, 16 lines md5sums Package: hmmer-doc Source: hmmer Version: 3.4+dfsg-3 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 1335 Recommends: hmmer (>= 3.4+dfsg-3), evince | pdf-viewer Section: doc Priority: optional Multi-Arch: foreign Homepage: http://hmmer.org/ Description: profile hidden Markov models for protein sequence analysis (docs) 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 the documentation and a tutorial for the hmmer package. drwxr-xr-x root/root 0 2025-09-29 12:45 ./ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc-base/ -rw-r--r-- root/root 572 2025-09-29 12:45 ./usr/share/doc-base/hmmer-doc.hmmer drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer-doc/ -rw-r--r-- root/root 983 2025-09-29 12:45 ./usr/share/doc/hmmer-doc/changelog.Debian.gz -rw-r--r-- root/root 5159 2025-09-29 12:45 ./usr/share/doc/hmmer-doc/copyright drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/ -rw-r--r-- root/root 603834 2023-08-15 18:30 ./usr/share/doc/hmmer/Userguide.pdf.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/tutorial/ -rw-r--r-- root/root 19087 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/7LESS_DROME -rw-r--r-- root/root 183 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/HBB_HUMAN -rw-r--r-- root/root 14842 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/MADE1.hmm -rw-r--r-- root/root 35454 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/MADE1.sto -rw-r--r-- root/root 122014 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/Pkinase.hmm -rw-r--r-- root/root 67852 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/Pkinase.sto -rw-r--r-- root/root 335516 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/dna_target.fa -rw-r--r-- root/root 41101 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/fn3.hmm -rw-r--r-- root/root 24538 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/fn3.sto -rw-r--r-- root/root 70298 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/globins4.hmm -rw-r--r-- root/root 863 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/globins4.sto -rw-r--r-- root/root 7210 2023-08-15 18:26 ./usr/share/doc/hmmer/tutorial/globins45.fa hmmer-examples_3.4+dfsg-3_amd64.deb ----------------------------------- new Debian package, version 2.0. size 32825788 bytes: control archive=18332 bytes. 864 bytes, 22 lines control 68891 bytes, 749 lines md5sums Package: hmmer-examples Source: hmmer Version: 3.4+dfsg-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 33761 Depends: libperl4-corelibs-perl Section: doc Priority: optional Multi-Arch: foreign Homepage: http://hmmer.org/ Description: profile hidden Markov models for protein sequence analysis (examples) 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 example files to test the hmmer package. drwxr-xr-x root/root 0 2025-09-29 12:45 ./ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer-examples/ -rw-r--r-- root/root 981 2025-09-29 12:45 ./usr/share/doc/hmmer-examples/changelog.Debian.gz -rw-r--r-- root/root 5159 2025-09-29 12:45 ./usr/share/doc/hmmer-examples/copyright drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/ -rw-r--r-- root/root 117 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/.travis.yml -rw-r--r-- root/root 3642 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/LICENSE -rw-r--r-- root/root 4645 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/Makefile.gz -rw-r--r-- root/root 4427 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/Makefile.in.gz -rw-r--r-- root/root 1697 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/README.md -rw-r--r-- root/root 14946 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/config.guess.gz -rw-r--r-- root/root 11857 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/config.sub.gz -rw-r--r-- root/root 7049 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/configure.ac.gz -rw-r--r-- root/root 571 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/decoy_config.h -rw-r--r-- root/root 494 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/decoy_config.h.in drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/demotic/ -rw-r--r-- root/root 1434 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/00README.gz -rwxr-xr-x root/root 126 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/blast2profmark -rwxr-xr-x root/root 121 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/blast2tbl -rw-r--r-- root/root 2858 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/demotic_blast.pm.gz -rw-r--r-- root/root 3674 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/demotic_fasta.pm.gz -rw-r--r-- root/root 1732 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/demotic_h2.pm.gz -rw-r--r-- root/root 1960 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/demotic_hmmer.pm.gz -rw-r--r-- root/root 3039 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/demotic_infernal_tab.pm.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/demotic/examples/ -rw-r--r-- root/root 364 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single-psiquery.fa -rw-r--r-- root/root 38302 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.asnt.gz -rw-r--r-- root/root 32076 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.fa.gz -rw-r--r-- root/root 2924 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.fa.phr.gz -rw-r--r-- root/root 1344 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.fa.pin -rw-r--r-- root/root 28195 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.fa.psq.gz -rw-r--r-- root/root 40593 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.pbl.gz -rw-r--r-- root/root 39592 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example-single.sto.gz -rw-r--r-- root/root 737 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.fa -rw-r--r-- root/root 69751 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.fasta.out.gz -rw-r--r-- root/root 35622 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.h2.out.gz -rw-r--r-- root/root 25445 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.hmm.gz -rw-r--r-- root/root 34920 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.hmm2.gz -rw-r--r-- root/root 163840 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.hmmsearch.out.gz -rw-r--r-- root/root 4768 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.ncbi-blastp.out.gz -rw-r--r-- root/root 47168 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.phmmer.out.gz -rw-r--r-- root/root 39454 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.psiblast.out.gz -rw-r--r-- root/root 71200 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.ssearch.out.gz -rw-r--r-- root/root 39766 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.sto.gz -rw-r--r-- root/root 89008 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/examples/example.wu-blastp.out.gz -rwxr-xr-x root/root 127 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/fasta2profmark -rwxr-xr-x root/root 121 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/fasta2tbl -rwxr-xr-x root/root 117 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/h22profmark -rwxr-xr-x root/root 112 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/h22tbl -rwxr-xr-x root/root 126 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/hmmer2profmark -rwxr-xr-x root/root 121 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/hmmer2tbl -rw-r--r-- root/root 4416 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/infernal_tab2gff.pl.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/demotic/regress/ -rw-r--r-- root/root 2432 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/fasta-profmark.out.gz -rw-r--r-- root/root 5344 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/fasta-tbl.out.gz -rw-r--r-- root/root 2363 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/h2-profmark.out.gz -rw-r--r-- root/root 3133 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/h2-tbl.out.gz -rw-r--r-- root/root 11385 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/hmmsearch-profmark.out.gz -rw-r--r-- root/root 13400 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/hmmsearch-tbl.out.gz -rw-r--r-- root/root 975 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/ncbi-blastp-profmark.out -rw-r--r-- root/root 2039 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/ncbi-blastp-tbl.out -rw-r--r-- root/root 2963 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/phmmer-profmark.out.gz -rw-r--r-- root/root 4730 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/phmmer-tbl.out.gz -rw-r--r-- root/root 1655 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/psiblast-profmark.out.gz -rw-r--r-- root/root 2633 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/psiblast-tbl.out.gz -rw-r--r-- root/root 2241 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/ssearch-profmark.out.gz -rw-r--r-- root/root 4963 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/ssearch-tbl.out.gz -rw-r--r-- root/root 6958 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/wu-blastp-profmark.out.gz -rw-r--r-- root/root 10482 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/regress/wu-blastp-tbl.out.gz -rwxr-xr-x root/root 446 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/demotic/test.pl drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/devkit/ -rw-r--r-- root/root 191 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/00README -rw-r--r-- root/root 3493 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/autodoc.gz -rw-r--r-- root/root 4026 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/autodoc.md.gz -rw-r--r-- root/root 2396 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/autodoc.py.gz -rwxr-xr-x root/root 2104 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/c2optlist -rwxr-xr-x root/root 3044 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/cexcerpt -rw-r--r-- root/root 1389 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/cexcerpt.man -rwxr-xr-x root/root 980 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/ctags-fix -rwxr-xr-x root/root 1047 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/man2optlist -rwxr-xr-x root/root 1705 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/rmanprocess.pl -rwxr-xr-x root/root 3067 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/rmanprocess.py -rwxr-xr-x root/root 2014 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/sedition -rwxr-xr-x root/root 2376 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/sedition-pp -rw-r--r-- root/root 8282 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/sqc.gz -rw-r--r-- root/root 3815 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/devkit/techtree.py.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/documentation/ -rw-r--r-- root/root 1694 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/documentation/Makefile.gz -rw-r--r-- root/root 1655 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/Makefile.in.gz -rw-r--r-- root/root 16159 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/codestyle.md.gz -rw-r--r-- root/root 22955 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/codestyle.tex.gz -rw-r--r-- root/root 357 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/copyright.tex -rw-r--r-- root/root 1812 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/doctricks.tex drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/documentation/figures/ -rw-r--r-- root/root 1287708 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/easel_techtree.ai.gz -rw-r--r-- root/root 1247213 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/easel_techtree.pdf.gz -rw-r--r-- root/root 177484 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/easel_techtree.png -rw-r--r-- root/root 30764 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/evd_basic.pdf.gz -rw-r--r-- root/root 31112 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/evd_location.pdf.gz -rw-r--r-- root/root 30515 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/evd_scale.pdf.gz -rw-r--r-- root/root 9239 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/gev_density.pdf.gz -rw-r--r-- root/root 14185 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/gev_logdensity.pdf.gz -rw-r--r-- root/root 173882 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rna_elements.ai.gz -rw-r--r-- root/root 227439 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rna_elements.eps.gz -rw-r--r-- root/root 9493 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rna_elements.pdf.gz -rw-r--r-- root/root 77312 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-bsu-alignment.ai.gz -rw-r--r-- root/root 502802 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-bsu-alignment.eps.gz -rw-r--r-- root/root 18660 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-bsu-alignment.pdf.gz -rw-r--r-- root/root 187895 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-ecoli.ai.gz -rw-r--r-- root/root 612530 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-ecoli.eps.gz -rw-r--r-- root/root 17446 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/figures/rnaseP-ecoli.pdf.gz -rw-r--r-- root/root 1887 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/format_a2m.tex.gz -rw-r--r-- root/root 3412 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/format_ncbi.tex.gz -rw-r--r-- root/root 3767 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/format_stockholm.tex.gz -rw-r--r-- root/root 3663 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/format_wuss.tex.gz -rw-r--r-- root/root 277 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/install.tex -rw-r--r-- root/root 67 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/installation.tex -rw-r--r-- root/root 5501 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/intro.tex.gz -rw-r--r-- root/root 2811 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/macros.tex -rw-r--r-- root/root 3697 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/main.tex.gz -rw-r--r-- root/root 3853 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/statistics.tex -rw-r--r-- root/root 556 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/titlepage.tex -rw-r--r-- root/root 867 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/documentation/typography.tex -rw-r--r-- root/root 29012 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/easel.c.gz -rw-r--r-- root/root 7441 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/easel.h.gz -rw-r--r-- root/root 7087 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/easel.tex.gz -rw-r--r-- root/root 48004 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/easel_utest.gz -rw-r--r-- root/root 3962 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alloc.c.gz -rw-r--r-- root/root 204 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alloc.h -rw-r--r-- root/root 2842 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alloc.md.gz -rw-r--r-- root/root 41298 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_alloc_utest.gz -rw-r--r-- root/root 20234 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alphabet.c.gz -rw-r--r-- root/root 2022 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alphabet.h.gz -rw-r--r-- root/root 8226 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_alphabet.tex.gz -rw-r--r-- root/root 48287 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_alphabet_utest.gz -rw-r--r-- root/root 1109 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_arr2.c -rw-r--r-- root/root 204 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_arr2.h -rw-r--r-- root/root 1463 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_arr3.c -rw-r--r-- root/root 226 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_arr3.h -rw-r--r-- root/root 2142 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_avx.c.gz -rw-r--r-- root/root 1648 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_avx.h.gz -rw-r--r-- root/root 1646 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_avx512.c.gz -rw-r--r-- root/root 1767 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_avx512.h.gz -rw-r--r-- root/root 3939 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_avx512_utest.gz -rw-r--r-- root/root 3941 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_avx_utest.gz -rw-r--r-- root/root 1677 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_bitfield.c.gz -rw-r--r-- root/root 867 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_bitfield.h -rw-r--r-- root/root 48292 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_bitfield_utest.gz -rw-r--r-- root/root 25402 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_buffer.c.gz -rw-r--r-- root/root 1574 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_buffer.h.gz -rw-r--r-- root/root 6748 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_buffer.tex.gz -rw-r--r-- root/root 85543 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_buffer_utest.gz -rw-r--r-- root/root 3973 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_cluster.c.gz -rw-r--r-- root/root 434 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_cluster.h -rw-r--r-- root/root 2197 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_cluster.tex -rw-r--r-- root/root 34202 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_cluster_utest.gz -rw-r--r-- root/root 1172 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_composition.c.gz -rw-r--r-- root/root 205 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_composition.h -rw-r--r-- root/root 2454 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_config.h -rw-r--r-- root/root 3011 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_config.h.in -rw-r--r-- root/root 3701 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_cpu.c.gz -rw-r--r-- root/root 257 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_cpu.h -rw-r--r-- root/root 4471 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_cpu_utest.gz -rw-r--r-- root/root 3010 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dirichlet.c.gz -rw-r--r-- root/root 934 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dirichlet.h -rw-r--r-- root/root 2343 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dirichlet.tex -rw-r--r-- root/root 53639 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_dirichlet_utest.gz -rw-r--r-- root/root 12592 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_distance.c.gz -rw-r--r-- root/root 2939 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_distance.h -rw-r--r-- root/root 2274 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_distance.tex.gz -rw-r--r-- root/root 242671 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_distance_utest.gz -rw-r--r-- root/root 12742 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dmatrix.c.gz -rw-r--r-- root/root 3860 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dmatrix.h -rw-r--r-- root/root 3343 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dmatrix.tex.gz -rw-r--r-- root/root 28220 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_dmatrix_utest.gz -rw-r--r-- root/root 21097 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dsqdata.c.gz -rw-r--r-- root/root 2515 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dsqdata.h.gz -rw-r--r-- root/root 5359 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dsqdata.md.gz -rw-r--r-- root/root 5197 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_dsqdata.tex.gz -rw-r--r-- root/root 372348 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_dsqdata_utest.gz -rw-r--r-- root/root 5412 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_exponential.c.gz -rw-r--r-- root/root 1570 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_exponential.h -rw-r--r-- root/root 1115 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_exponential.tex -rw-r--r-- root/root 40027 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_exponential_utest.gz -rw-r--r-- root/root 6547 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_fileparser.c.gz -rw-r--r-- root/root 2059 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_fileparser.h -rw-r--r-- root/root 1625 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_fileparser.tex.gz -rw-r--r-- root/root 20906 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_fileparser_utest.gz -rw-r--r-- root/root 8705 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gamma.c.gz -rw-r--r-- root/root 1555 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gamma.h -rw-r--r-- root/root 2353 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gamma.md.gz -rw-r--r-- root/root 1711 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gamma.tex -rw-r--r-- root/root 53975 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_gamma_utest.gz -rw-r--r-- root/root 11949 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gencode.c.gz -rw-r--r-- root/root 1727 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gencode.h.gz -rw-r--r-- root/root 137667 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_gencode_utest.gz -rw-r--r-- root/root 21653 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_getopts.c.gz -rw-r--r-- root/root 1903 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_getopts.h.gz -rw-r--r-- root/root 10835 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_getopts.md.gz -rw-r--r-- root/root 42178 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_getopts_utest.gz -rw-r--r-- root/root 7368 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gev.c.gz -rw-r--r-- root/root 1612 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gev.h -rw-r--r-- root/root 2765 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gev.tex.gz -rw-r--r-- root/root 3184 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_graph.c.gz -rw-r--r-- root/root 200 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_graph.h -rw-r--r-- root/root 51481 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_graph_utest.gz -rw-r--r-- root/root 10580 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gumbel.c.gz -rw-r--r-- root/root 1889 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gumbel.h -rw-r--r-- root/root 7312 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_gumbel.tex.gz -rw-r--r-- root/root 68330 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_gumbel_utest.gz -rw-r--r-- root/root 2991 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_heap.c.gz -rw-r--r-- root/root 1015 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_heap.h -rw-r--r-- root/root 42113 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_heap_utest.gz -rw-r--r-- root/root 17471 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_histogram.c.gz -rw-r--r-- root/root 1844 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_histogram.h.gz -rw-r--r-- root/root 4799 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_histogram.tex.gz -rw-r--r-- root/root 86923 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_histogram_utest.gz -rw-r--r-- root/root 5850 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_hmm.c.gz -rw-r--r-- root/root 2341 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_hmm.h -rw-r--r-- root/root 62333 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_hmm_utest.gz -rw-r--r-- root/root 10384 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_huffman.c.gz -rw-r--r-- root/root 1931 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_huffman.h -rw-r--r-- root/root 61432 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_huffman_utest.gz -rw-r--r-- root/root 9849 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_hyperexp.c.gz -rw-r--r-- root/root 2472 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_hyperexp.h -rw-r--r-- root/root 1101 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_hyperexp.tex -rw-r--r-- root/root 76319 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_hyperexp_utest.gz -rw-r--r-- root/root 12938 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_iset.c.gz -rw-r--r-- root/root 2097 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_iset.h -rw-r--r-- root/root 212503 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_iset_utest.gz -rw-r--r-- root/root 14553 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_json.c.gz -rw-r--r-- root/root 2008 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_json.h.gz -rw-r--r-- root/root 79630 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_json_utest.gz -rw-r--r-- root/root 7462 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_keyhash.c.gz -rw-r--r-- root/root 2755 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_keyhash.h -rw-r--r-- root/root 3621 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_keyhash.tex -rw-r--r-- root/root 55038 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_keyhash_utest.gz -rw-r--r-- root/root 2638 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_lognormal.c.gz -rw-r--r-- root/root 634 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_lognormal.h -rw-r--r-- root/root 916 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_lognormal.md -rw-r--r-- root/root 45447 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_lognormal_utest.gz -rw-r--r-- root/root 3454 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_matrixops.c.gz -rw-r--r-- root/root 2831 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_matrixops.h -rw-r--r-- root/root 54015 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_matrixops_utest.gz -rw-r--r-- root/root 11663 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mem.c.gz -rw-r--r-- root/root 1702 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mem.h -rw-r--r-- root/root 3063 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mem.md -rw-r--r-- root/root 58110 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_mem_utest.gz -rw-r--r-- root/root 10314 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_minimizer.c.gz -rw-r--r-- root/root 2773 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_minimizer.h -rw-r--r-- root/root 241 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_minimizer.tex -rw-r--r-- root/root 55588 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_minimizer_utest.gz -rw-r--r-- root/root 8871 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mixdchlet.c.gz -rw-r--r-- root/root 1883 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mixdchlet.h -rw-r--r-- root/root 3438 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mixdchlet.tex -rw-r--r-- root/root 97861 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_mixdchlet_utest.gz -rw-r--r-- root/root 6308 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mixgev.c.gz -rw-r--r-- root/root 2090 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mixgev.h -rw-r--r-- root/root 10488 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mpi.c.gz -rw-r--r-- root/root 2784 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mpi.h -rw-r--r-- root/root 770 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_mpi.tex -rw-r--r-- root/root 30152 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa.c.gz -rw-r--r-- root/root 2907 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa.h.gz -rw-r--r-- root/root 4446 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa.tex.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/a2m/ -rw-r--r-- root/root 682 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/a2m/a2m.good.1 -rw-r--r-- root/root 409 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/a2m/a2m.good.2 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/afa/ -rw-r--r-- root/root 717 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/afa/afa.good.1 -rw-r--r-- root/root 410 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/afa/afa.good.2 -rw-r--r-- root/root 909 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/afa/afa.good.3 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/clustal/ -rw-r--r-- root/root 1125 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/clustal/clustal.good.1 -rw-r--r-- root/root 689 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/clustal/clustal.good.2 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/ -rw-r--r-- root/root 139 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.ambig.1 -rw-r--r-- root/root 76 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.1 -rw-r--r-- root/root 116 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.10 -rw-r--r-- root/root 141 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.11 -rw-r--r-- root/root 77 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.2 -rw-r--r-- root/root 73 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.3 -rw-r--r-- root/root 68 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.4 -rw-r--r-- root/root 9 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.5 -rw-r--r-- root/root 39 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.6 -rw-r--r-- root/root 74 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.7 -rw-r--r-- root/root 73 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.8 -rw-r--r-- root/root 72 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.bad.9 -rw-r--r-- root/root 296 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.good.1 -rw-r--r-- root/root 441 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.good.2 -rw-r--r-- root/root 1575 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylip/phylip.good.3 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylips/ -rw-r--r-- root/root 295 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylips/phylips.good.1 -rw-r--r-- root/root 1205 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/phylips/phylips.good.2 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/psiblast/ -rw-r--r-- root/root 818 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/psiblast/psiblast.good.1 -rw-r--r-- root/root 446 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/psiblast/psiblast.good.2 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/ -rw-r--r-- root/root 1472 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/00MANIFEST -rw-r--r-- root/root 44 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.1 -rw-r--r-- root/root 328 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.10 -rw-r--r-- root/root 327 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.11 -rw-r--r-- root/root 327 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.12 -rw-r--r-- root/root 327 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.13 -rw-r--r-- root/root 274 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.14 -rw-r--r-- root/root 241 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.2 -rw-r--r-- root/root 163 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.3 -rw-r--r-- root/root 169 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.4 -rw-r--r-- root/root 196 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.5 -rw-r--r-- root/root 190 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.6 -rw-r--r-- root/root 298 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.7 -rw-r--r-- root/root 190 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.8 -rw-r--r-- root/root 326 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.bad.9 -rw-r--r-- root/root 130 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.good.1 -rw-r--r-- root/root 974 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.good.2 -rw-r--r-- root/root 420 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.good.3 -rw-r--r-- root/root 557 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/selex/selex.good.4 drwxr-xr-x root/root 0 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/ -rw-r--r-- root/root 25 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.1 -rw-r--r-- root/root 102 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.2 -rw-r--r-- root/root 84 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.3 -rw-r--r-- root/root 75 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.4 -rw-r--r-- root/root 30 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.5 -rw-r--r-- root/root 81 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.6 -rw-r--r-- root/root 86 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.7 -rw-r--r-- root/root 55 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.bad.8 -rw-r--r-- root/root 3271 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msa_testfiles/stockholm/stockholm.good.1 -rw-r--r-- root/root 270369 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msa_utest.gz -rw-r--r-- root/root 4584 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msacluster.c.gz -rw-r--r-- root/root 318 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msacluster.h -rw-r--r-- root/root 954 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msacluster.tex -rw-r--r-- root/root 198941 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msacluster_utest.gz -rw-r--r-- root/root 16318 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile.c.gz -rw-r--r-- root/root 2419 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile.h.gz -rw-r--r-- root/root 2757 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile.md.gz -rw-r--r-- root/root 15456 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile2.c.gz -rw-r--r-- root/root 3333 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile2.h -rw-r--r-- root/root 218806 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile2_utest.gz -rw-r--r-- root/root 11516 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_a2m.c.gz -rw-r--r-- root/root 539 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_a2m.h -rw-r--r-- root/root 219558 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_a2m_utest.gz -rw-r--r-- root/root 7677 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_afa.c.gz -rw-r--r-- root/root 533 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_afa.h -rw-r--r-- root/root 209517 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_afa_utest.gz -rw-r--r-- root/root 11497 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_clustal.c.gz -rw-r--r-- root/root 573 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_clustal.h -rw-r--r-- root/root 218546 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_clustal_utest.gz -rw-r--r-- root/root 17617 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_phylip.c.gz -rw-r--r-- root/root 686 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_phylip.h -rw-r--r-- root/root 250755 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_phylip_utest.gz -rw-r--r-- root/root 8634 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_psiblast.c.gz -rw-r--r-- root/root 559 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_psiblast.h -rw-r--r-- root/root 213030 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_psiblast_utest.gz -rw-r--r-- root/root 11303 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_selex.c.gz -rw-r--r-- root/root 542 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_selex.h -rw-r--r-- root/root 224364 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_selex_utest.gz -rw-r--r-- root/root 18564 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_stockholm.c.gz -rw-r--r-- root/root 573 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msafile_stockholm.h -rw-r--r-- root/root 226948 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_stockholm_utest.gz -rw-r--r-- root/root 266956 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msafile_utest.gz -rw-r--r-- root/root 5474 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msashuffle.c.gz -rw-r--r-- root/root 1115 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msashuffle.h -rw-r--r-- root/root 18478 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msaweight.c.gz -rw-r--r-- root/root 3609 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msaweight.h -rw-r--r-- root/root 2375 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msaweight.md.gz -rw-r--r-- root/root 1809 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_msaweight.tex -rw-r--r-- root/root 252814 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_msaweight_utest.gz -rw-r--r-- root/root 7421 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_neon.c.gz -rw-r--r-- root/root 2918 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_neon.h.gz -rw-r--r-- root/root 2611 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_neon_utest.gz -rw-r--r-- root/root 2800 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_normal.c.gz -rw-r--r-- root/root 672 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_normal.h -rw-r--r-- root/root 694 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_normal.tex -rw-r--r-- root/root 14110 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_normal_utest.gz -rw-r--r-- root/root 2154 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_paml.c.gz -rw-r--r-- root/root 504 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_paml.h -rw-r--r-- root/root 132 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_paml.tex -rw-r--r-- root/root 2450 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_quicksort.c.gz -rw-r--r-- root/root 270 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_quicksort.h -rw-r--r-- root/root 39934 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_quicksort_utest.gz -rw-r--r-- root/root 8949 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_rand64.c.gz -rw-r--r-- root/root 1167 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_rand64.h -rw-r--r-- root/root 53702 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_rand64_utest.gz -rw-r--r-- root/root 14663 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_random.c.gz -rw-r--r-- root/root 2709 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_random.h -rw-r--r-- root/root 2565 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_random.tex.gz -rw-r--r-- root/root 61865 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_random_utest.gz -rw-r--r-- root/root 15105 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_randomseq.c.gz -rw-r--r-- root/root 3366 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_randomseq.h -rw-r--r-- root/root 3994 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_randomseq.tex -rw-r--r-- root/root 93854 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_randomseq_utest.gz -rw-r--r-- root/root 7216 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_ratematrix.c.gz -rw-r--r-- root/root 1145 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_ratematrix.h -rw-r--r-- root/root 111 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_ratematrix.tex -rw-r--r-- root/root 36581 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_ratematrix_utest.gz -rw-r--r-- root/root 8620 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_recorder.c.gz -rw-r--r-- root/root 3206 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_recorder.h -rw-r--r-- root/root 55407 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_recorder_utest.gz -rw-r--r-- root/root 5474 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_red_black.c.gz -rw-r--r-- root/root 3357 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_red_black.h -rw-r--r-- root/root 26761 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_red_black_utest.gz -rw-r--r-- root/root 16822 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_regexp.c.gz -rw-r--r-- root/root 2952 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_regexp.h -rw-r--r-- root/root 2592 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_regexp.md.gz -rw-r--r-- root/root 5218 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_regexp.tex.gz -rw-r--r-- root/root 61993 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_regexp_utest.gz -rw-r--r-- root/root 3700 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_rootfinder.c.gz -rw-r--r-- root/root 1416 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_rootfinder.h -rw-r--r-- root/root 1900 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_rootfinder.tex -rw-r--r-- root/root 15369 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_rootfinder_utest.gz -rw-r--r-- root/root 25452 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_scorematrix.c.gz -rw-r--r-- root/root 3698 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_scorematrix.h -rw-r--r-- root/root 3033 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_scorematrix.tex -rw-r--r-- root/root 85791 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_scorematrix_utest.gz -rw-r--r-- root/root 20270 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sq.c.gz -rw-r--r-- root/root 3877 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sq.h.gz -rw-r--r-- root/root 5703 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sq.tex.gz -rw-r--r-- root/root 204598 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_sq_utest.gz -rw-r--r-- root/root 20138 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio.c.gz -rw-r--r-- root/root 2144 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio.h.gz -rw-r--r-- root/root 4496 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio.tex.gz -rw-r--r-- root/root 28776 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio_ascii.c.gz -rw-r--r-- root/root 3851 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio_ascii.h -rw-r--r-- root/root 20797 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio_ncbi.c.gz -rw-r--r-- root/root 1332 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sqio_ncbi.h.gz -rw-r--r-- root/root 436258 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_sqio_utest.gz -rw-r--r-- root/root 8061 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sse.c.gz -rw-r--r-- root/root 2878 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sse.h.gz -rw-r--r-- root/root 1493 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_sse.tex -rw-r--r-- root/root 54917 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_sse_utest.gz -rw-r--r-- root/root 19832 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_ssi.c.gz -rw-r--r-- root/root 1940 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_ssi.h.gz -rw-r--r-- root/root 7092 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_ssi.tex.gz -rw-r--r-- root/root 404187 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_ssi_utest.gz -rw-r--r-- root/root 7756 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stack.c.gz -rw-r--r-- root/root 2290 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stack.h -rw-r--r-- root/root 1495 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stack.tex.gz -rw-r--r-- root/root 53788 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_stack_utest.gz -rw-r--r-- root/root 14373 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stats.c.gz -rw-r--r-- root/root 1551 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stats.h.gz -rw-r--r-- root/root 1706 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stats.tex -rw-r--r-- root/root 72623 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_stats_utest.gz -rw-r--r-- root/root 4208 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stopwatch.c.gz -rw-r--r-- root/root 1702 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stopwatch.h -rw-r--r-- root/root 1853 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stopwatch.tex.gz -rw-r--r-- root/root 5199 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stretchexp.c.gz -rw-r--r-- root/root 1593 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stretchexp.h -rw-r--r-- root/root 1494 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_stretchexp.tex -rw-r--r-- root/root 80280 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_stretchexp_utest.gz -rw-r--r-- root/root 3586 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_subcmd.c -rw-r--r-- root/root 632 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_subcmd.h -rw-r--r-- root/root 2325 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_swat.c.gz -rw-r--r-- root/root 77 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_swat.tex -rw-r--r-- root/root 4401 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_threads.c.gz -rw-r--r-- root/root 1588 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_threads.h -rw-r--r-- root/root 18023 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_tree.c.gz -rw-r--r-- root/root 1851 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_tree.h.gz -rw-r--r-- root/root 1283 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_tree.tex -rw-r--r-- root/root 71331 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_tree_utest.gz -rw-r--r-- root/root 7262 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_varint.c.gz -rw-r--r-- root/root 805 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_varint.h -rw-r--r-- root/root 4116 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_varint.md.gz -rw-r--r-- root/root 51619 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_varint_utest.gz -rw-r--r-- root/root 11186 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_vectorops.c.gz -rw-r--r-- root/root 1168 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_vectorops.h.gz -rw-r--r-- root/root 1861 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_vectorops.md.gz -rw-r--r-- root/root 65435 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_vectorops_utest.gz -rw-r--r-- root/root 6218 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_vmx.c.gz -rw-r--r-- root/root 1468 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_vmx.h.gz -rw-r--r-- root/root 2613 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_vmx_utest.gz -rw-r--r-- root/root 5795 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_weibull.c.gz -rw-r--r-- root/root 1554 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_weibull.h -rw-r--r-- root/root 1458 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_weibull.tex -rw-r--r-- root/root 75653 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_weibull_utest.gz -rw-r--r-- root/root 3930 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_workqueue.c.gz -rw-r--r-- root/root 3762 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_workqueue.h -rw-r--r-- root/root 7247 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_wuss.c.gz -rw-r--r-- root/root 561 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_wuss.h -rw-r--r-- root/root 1172 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/esl_wuss.tex -rw-r--r-- root/root 34182 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/esl_wuss_utest.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/formats/ -rw-r--r-- root/root 2122 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/BLOSUM62 -rw-r--r-- root/root 2015 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/embl.gz -rw-r--r-- root/root 712 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta -rw-r--r-- root/root 718 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta.2 -rw-r--r-- root/root 46 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta.bad.1 -rw-r--r-- root/root 14 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta.bad.2 -rw-r--r-- root/root 23 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta.bad.3 -rw-r--r-- root/root 60 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/fasta.odd.1 -rw-r--r-- root/root 2490 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/genbank -rw-r--r-- root/root 2249 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/genbank.2 -rw-r--r-- root/root 2491 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/genbank.bad.1 -rw-r--r-- root/root 44 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/stockholm.1 -rw-r--r-- root/root 4342 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/uniprot.gz -rw-r--r-- root/root 3019 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/formats/wag.dat -rw-r--r-- root/root 3447 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/install-sh.gz -rw-r--r-- root/root 1523 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/interface_gsl.c -rw-r--r-- root/root 538 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/interface_gsl.h -rw-r--r-- root/root 2558 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/interface_lapack.c -rw-r--r-- root/root 784 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/interface_lapack.h -rw-r--r-- root/root 3876538 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/libeasel.a.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/m4/ -rw-r--r-- root/root 3330 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_check_compile_flag.m4 -rw-r--r-- root/root 3418 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_check_gnu_make.m4 -rw-r--r-- root/root 3604 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_compiler_vendor.m4 -rw-r--r-- root/root 1774 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_gcc_func_attribute.m4.gz -rw-r--r-- root/root 2405 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_prog_cc_mpi.m4.gz -rw-r--r-- root/root 7127 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/ax_pthread.m4.gz -rw-r--r-- root/root 2424 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_avx.m4 -rw-r--r-- root/root 3145 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_avx512.m4 -rw-r--r-- root/root 1093 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_cuda.m4 -rw-r--r-- root/root 3527 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_neon.m4 -rw-r--r-- root/root 1737 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_pic_flags.m4.gz -rw-r--r-- root/root 2472 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_sse.m4 -rw-r--r-- root/root 2571 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_sse4.m4 -rw-r--r-- root/root 2011 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/m4/esl_vmx.m4 -rwxr-xr-x root/root 792 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/makeTAGS.sh drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/ -rw-r--r-- root/root 3533 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/Makefile -rw-r--r-- root/root 3264 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/Makefile.in -rw-r--r-- root/root 1972 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/cmd_alistat.c.gz -rw-r--r-- root/root 3342 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/cmd_downsample.c.gz -rw-r--r-- root/root 2652 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/cmd_filter.c.gz -rw-r--r-- root/root 3502 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/cmd_filter.md.gz -rw-r--r-- root/root 2256 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/cmd_index.c.gz -rw-r--r-- root/root 3287 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/easel-downsample.man.in -rw-r--r-- root/root 1672 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/easel.c.gz -rw-r--r-- root/root 538691 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/easel.gz -rw-r--r-- root/root 4000 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-afetch.c.gz -rw-r--r-- root/root 285160 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-afetch.gz -rw-r--r-- root/root 1224 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-afetch.itest.pl.gz -rw-r--r-- root/root 2391 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-afetch.man -rw-r--r-- root/root 2325 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-afetch.man.in -rw-r--r-- root/root 33624 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimanip.c.gz -rw-r--r-- root/root 527335 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimanip.gz -rw-r--r-- root/root 2073 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimanip.itest.pl.gz -rw-r--r-- root/root 2914 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimanip.man.gz -rw-r--r-- root/root 2865 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimanip.man.in.gz -rw-r--r-- root/root 7271 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimap.c.gz -rw-r--r-- root/root 228861 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimap.gz -rw-r--r-- root/root 1124 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimap.itest.pl.gz -rw-r--r-- root/root 1837 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimap.man.gz -rw-r--r-- root/root 1782 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimap.man.in.gz -rw-r--r-- root/root 14370 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimask.c.gz -rw-r--r-- root/root 352036 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimask.gz -rw-r--r-- root/root 2306 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimask.itest.pl.gz -rw-r--r-- root/root 4778 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimask.man.gz -rw-r--r-- root/root 4727 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimask.man.in.gz -rw-r--r-- root/root 18780 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimerge.c.gz -rw-r--r-- root/root 352788 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimerge.gz -rw-r--r-- root/root 1669 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimerge.itest.pl.gz -rw-r--r-- root/root 2058 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimerge.man.gz -rw-r--r-- root/root 2008 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alimerge.man.in.gz -rw-r--r-- root/root 3729 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alipid.c -rw-r--r-- root/root 236705 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alipid.gz -rw-r--r-- root/root 3235 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alipid.man -rw-r--r-- root/root 3169 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alipid.man.in -rw-r--r-- root/root 3575 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alirev.c -rw-r--r-- root/root 261023 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alirev.gz -rw-r--r-- root/root 3388 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alirev.man -rw-r--r-- root/root 3322 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alirev.man.in -rw-r--r-- root/root 10560 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alistat.c.gz -rw-r--r-- root/root 307700 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alistat.gz -rw-r--r-- root/root 1701 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alistat.itest.pl.gz -rw-r--r-- root/root 2097 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alistat.man.gz -rw-r--r-- root/root 2046 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-alistat.man.in.gz -rw-r--r-- root/root 6347 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compalign.c.gz -rw-r--r-- root/root 233446 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compalign.gz -rw-r--r-- root/root 1175 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compalign.itest.pl.gz -rw-r--r-- root/root 1743 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compalign.man.gz -rw-r--r-- root/root 1689 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compalign.man.in.gz -rw-r--r-- root/root 3877 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compstruct.c.gz -rw-r--r-- root/root 206279 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compstruct.gz -rw-r--r-- root/root 3413 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compstruct.man -rw-r--r-- root/root 3347 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-compstruct.man.in -rw-r--r-- root/root 7540 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-construct.c.gz -rw-r--r-- root/root 256533 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-construct.gz -rw-r--r-- root/root 1205 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-construct.itest.pl.gz -rw-r--r-- root/root 1792 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-construct.man.gz -rw-r--r-- root/root 1734 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-construct.man.in.gz -rw-r--r-- root/root 3068 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-histplot.c.gz -rw-r--r-- root/root 99408 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-histplot.gz -rw-r--r-- root/root 1355 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-histplot.man -rw-r--r-- root/root 1289 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-histplot.man.in -rw-r--r-- root/root 3213 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mask.c.gz -rw-r--r-- root/root 387255 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mask.gz -rw-r--r-- root/root 728 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mask.itest.pl.gz -rw-r--r-- root/root 3457 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mask.man -rw-r--r-- root/root 3380 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mask.man.in -rw-r--r-- root/root 3164 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mixdchlet.c.gz -rw-r--r-- root/root 102575 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mixdchlet.gz -rw-r--r-- root/root 3904 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mixdchlet.man -rw-r--r-- root/root 3838 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-mixdchlet.man.in -rw-r--r-- root/root 11089 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-reformat.c.gz -rw-r--r-- root/root 458490 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-reformat.gz -rw-r--r-- root/root 2411 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-reformat.man.gz -rw-r--r-- root/root 2359 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-reformat.man.in.gz -rw-r--r-- root/root 3584 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-selectn.c -rw-r--r-- root/root 41069 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-selectn.gz -rw-r--r-- root/root 1352 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-selectn.man -rw-r--r-- root/root 1286 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-selectn.man.in -rw-r--r-- root/root 2472 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqrange.c.gz -rw-r--r-- root/root 378157 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqrange.gz -rw-r--r-- root/root 960 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqrange.itest.pl.gz -rw-r--r-- root/root 1789 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqrange.man -rw-r--r-- root/root 1723 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqrange.man.in -rw-r--r-- root/root 3085 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqstat.c.gz -rw-r--r-- root/root 382325 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqstat.gz -rw-r--r-- root/root 1877 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqstat.man -rw-r--r-- root/root 1811 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-seqstat.man.in -rw-r--r-- root/root 5885 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-sfetch.c.gz -rw-r--r-- root/root 440752 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-sfetch.gz -rw-r--r-- root/root 2282 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-sfetch.man.gz -rw-r--r-- root/root 2232 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-sfetch.man.in.gz -rw-r--r-- root/root 4432 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-shuffle.c.gz -rw-r--r-- root/root 448487 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-shuffle.gz -rwxr-xr-x root/root 3053 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-shuffle.itest.py -rw-r--r-- root/root 1899 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-shuffle.man.gz -rw-r--r-- root/root 1849 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-shuffle.man.in.gz -rw-r--r-- root/root 66560 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-ssdraw.c.gz -rw-r--r-- root/root 440801 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-ssdraw.gz -rw-r--r-- root/root 3682 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-ssdraw.itest.pl.gz -rw-r--r-- root/root 8408 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-ssdraw.man.gz -rw-r--r-- root/root 8361 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-ssdraw.man.in.gz -rw-r--r-- root/root 2923 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-translate.c.gz -rw-r--r-- root/root 429810 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-translate.gz -rw-r--r-- root/root 2190 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-translate.itest.pl.gz -rw-r--r-- root/root 3125 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-translate.man.gz -rw-r--r-- root/root 3080 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-translate.man.in.gz -rw-r--r-- root/root 1839 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-weight.c.gz -rw-r--r-- root/root 299042 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-weight.gz -rw-r--r-- root/root 1905 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-weight.man -rw-r--r-- root/root 1839 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/miniapps/esl-weight.man.in drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/release-notes/ -rw-r--r-- root/root 2375 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/release-notes/RELEASE-0.46.md.gz -rw-r--r-- root/root 994 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/release-notes/RELEASE-0.47.md -rw-r--r-- root/root 330 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/release-notes/RELEASE-0.48.md -rw-r--r-- root/root 2596 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/release-notes/RELEASE-0.49.md drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/testsuite/ -rw-r--r-- root/root 2564 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/easel/testsuite/Makefile -rw-r--r-- root/root 2385 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/Makefile.in -rw-r--r-- root/root 1682 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/coverage_report.pl.gz -rwxr-xr-x root/root 671 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/e2.sh -rw-r--r-- root/root 1294 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/i1-degen-residues.pl.gz -rw-r--r-- root/root 2697 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/i2-ncbi-indices.pl.gz -rwxr-xr-x root/root 2574 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/i3-blank-gf.pl -rwxr-xr-x root/root 1989 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/i4-alimanip-sindi.sh -rwxr-xr-x root/root 2935 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/parse_test_results.py -rw-r--r-- root/root 1705 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/testsuite.sqc.gz -rw-r--r-- root/root 1109 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/trna-5.stk -rw-r--r-- root/root 1363 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/trna-ssdraw.ps.gz -rwxr-xr-x root/root 3294 2023-08-13 08:10 ./usr/share/doc/hmmer/examples/easel/testsuite/valgrind_report.pl drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/ -rw-r--r-- root/root 296711 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/build_utest.gz -rw-r--r-- root/root 142606 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/generic_fwdback_chk_utest.gz -rw-r--r-- root/root 143766 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/generic_fwdback_utest.gz -rw-r--r-- root/root 104209 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/generic_msv_utest.gz -rw-r--r-- root/root 137411 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/generic_stotrace_utest.gz -rw-r--r-- root/root 305014 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/generic_viterbi_utest.gz -rw-r--r-- root/root 24631 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/hmmd_search_status_utest.gz -rw-r--r-- root/root 42726 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/hmmer_utest.gz -rw-r--r-- root/root 843133 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/hmmpgmd2msa_utest.gz -rwxr-xr-x root/root 2286 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/hmmpress.itest.pl drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/ -rw-r--r-- root/root 146669 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/decoding_utest.gz -rw-r--r-- root/root 134028 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/fwdback_utest.gz -rw-r--r-- root/root 655138 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/io_utest.gz -rw-r--r-- root/root 491524 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/msvfilter_utest.gz -rw-r--r-- root/root 154316 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/null2_utest.gz -rw-r--r-- root/root 211809 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/optacc_utest.gz -rw-r--r-- root/root 174667 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/stotrace_utest.gz -rw-r--r-- root/root 130179 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/impl/vitfilter_utest.gz -rw-r--r-- root/root 171396 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/itest_brute.gz -rw-r--r-- root/root 41983 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/logsum_utest.gz -rw-r--r-- root/root 63989 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/modelconfig_utest.gz -rw-r--r-- root/root 126745 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_alidisplay_utest.gz -rw-r--r-- root/root 77102 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_bg_utest.gz -rw-r--r-- root/root 89375 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_domain_utest.gz -rw-r--r-- root/root 99024 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_gmx_utest.gz -rw-r--r-- root/root 91803 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_gmxchk_utest.gz -rw-r--r-- root/root 108276 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_hit_utest.gz -rw-r--r-- root/root 89054 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_hmm_utest.gz -rw-r--r-- root/root 28551 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_hmmd_search_stats_utest.gz -rw-r--r-- root/root 595203 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_hmmfile_utest.gz -rw-r--r-- root/root 83748 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_profile_utest.gz -rw-r--r-- root/root 83404 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_scoredata_utest.gz -rw-r--r-- root/root 189978 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_tophits_utest.gz -rw-r--r-- root/root 271664 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/p7_trace_utest.gz -rw-r--r-- root/root 207943 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/src/seqmodel_utest.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/testsuite/ -rw-r--r-- root/root 165 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.afa -rw-r--r-- root/root 132 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.fa -rw-r--r-- root/root 176 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.phr -rw-r--r-- root/root 112 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.pin -rw-r--r-- root/root 48 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.pog -rw-r--r-- root/root 80 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.psd -rw-r--r-- root/root 64 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.psi -rw-r--r-- root/root 104 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.psq -rw-r--r-- root/root 180 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa-alitest.sto -rw-r--r-- root/root 2319 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa.hmm.gz -rw-r--r-- root/root 353 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/20aa.sto -rw-r--r-- root/root 5477 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/2OG-FeII_Oxy_3-nt.hmm.gz -rw-r--r-- root/root 11353 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/2OG-FeII_Oxy_3.hmm.gz -rw-r--r-- root/root 2970 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.fa.gz -rw-r--r-- root/root 45 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nhr -rw-r--r-- root/root 96 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nin -rw-r--r-- root/root 36 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nog -rw-r--r-- root/root 22 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nsd -rw-r--r-- root/root 65 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nsi -rw-r--r-- root/root 2497 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box-alitest.nsq -rw-r--r-- root/root 826 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box.hmm.gz -rw-r--r-- root/root 1022 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/3box.sto -rw-r--r-- root/root 14102 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/Caudal_act.hmm.gz -rw-r--r-- root/root 2009 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/Caudal_act.sto.gz -rw-r--r-- root/root 36100 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/LuxC.hmm.gz -rw-r--r-- root/root 4396 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/LuxC.sto.gz -rw-r--r-- root/root 1450 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/M1.hmm -rw-r--r-- root/root 38 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/M1.sto -rw-r--r-- root/root 1093 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/testsuite/Makefile -rw-r--r-- root/root 1145 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/Makefile.in -rw-r--r-- root/root 539 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/PAX8_HUMAN -rw-r--r-- root/root 3552 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/PSE.hmm -rw-r--r-- root/root 846 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/PSE.sto -rw-r--r-- root/root 70531 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/Patched.hmm.gz -rw-r--r-- root/root 6942 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/Patched.sto.gz -rw-r--r-- root/root 7585 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/RRM_1.hmm.gz -rw-r--r-- root/root 7329 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/RRM_1.sto.gz -rw-r--r-- root/root 103062 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/SMC_N.hmm.gz -rw-r--r-- root/root 22557 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/SMC_N.sto.gz -rw-r--r-- root/root 3399 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/XYPPX.hmm -rw-r--r-- root/root 1866 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/XYPPX.sto -rw-r--r-- root/root 14 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/ecori.fa -rw-r--r-- root/root 1624 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/ecori.hmm -rw-r--r-- root/root 44 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/ecori.sto -rw-r--r-- root/root 2917 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/h3.pm -rwxr-xr-x root/root 1828 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i1-build-variation.sh -rwxr-xr-x root/root 3418 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i10-duplicate-names.pl -rwxr-xr-x root/root 2513 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i11-hmmalign-mapali.pl -rwxr-xr-x root/root 2063 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i12-delete-corruption.pl -rwxr-xr-x root/root 3938 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i13-msa-integrity.pl -rwxr-xr-x root/root 2724 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i14-hmmemit-consensus.pl -rw-r--r-- root/root 2408 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i15-hmmconvert.pl.gz -rwxr-xr-x root/root 1147 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i16-build-allins.pl -rw-r--r-- root/root 2950 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i17-stdin.pl.gz -rw-r--r-- root/root 1640 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i18-nhmmer-generic.pl.gz -rw-r--r-- root/root 41012 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/testsuite/i19-hmmpgmd-ga.pl.gz -rwxr-xr-x root/root 1530 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i2-search-variation.sh -rw-r--r-- root/root 1754 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i20-fmindex-core.pl.gz -rw-r--r-- root/root 1507 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i21-rewind.pl.gz -rw-r--r-- root/root 40542 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i22-hmmpgmd-shard-ga.pl.gz -rwxr-xr-x root/root 1122 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i23-bad-fasta.sh -rwxr-xr-x root/root 2317 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i3-seqsearch-variation.sh -rwxr-xr-x root/root 1655 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i4-zerolength-seqs.sh -rwxr-xr-x root/root 2998 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i5-hmmbuild-naming.pl -rwxr-xr-x root/root 1885 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i6-hmmalign-mapali.pl -rwxr-xr-x root/root 1243 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i7-hmmbuild-fragments.pl -rwxr-xr-x root/root 3162 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i8-nonresidues.pl -rw-r--r-- root/root 1186 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/i9-optional-annotation.pl.gz -rw-r--r-- root/root 3008 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/iss159-nhmmer-overlap.py.gz -rw-r--r-- root/root 8248 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/minifam.gz -rwxr-xr-x root/root 2938 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/parse_test_results.py -rw-r--r-- root/root 2497 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/rndseq400-10.fa.gz -rw-r--r-- root/root 5618 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/testsuite/testsuite.sqc.gz drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/examples/tutorial/ -rw-r--r-- root/root 19087 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/7LESS_DROME -rw-r--r-- root/root 183 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/HBB_HUMAN -rw-r--r-- root/root 14842 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/MADE1.hmm -rw-r--r-- root/root 35454 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/MADE1.sto -rw-r--r-- root/root 122014 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/Pkinase.hmm -rw-r--r-- root/root 67852 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/Pkinase.sto -rw-r--r-- root/root 335516 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/dna_target.fa -rw-r--r-- root/root 41101 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/fn3.hmm -rw-r--r-- root/root 24538 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/fn3.sto -rw-r--r-- root/root 70298 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/globins4.hmm -rw-r--r-- root/root 863 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/globins4.sto -rw-r--r-- root/root 7210 2023-08-15 18:26 ./usr/share/doc/hmmer/examples/tutorial/globins45.fa hmmer_3.4+dfsg-3_amd64.deb -------------------------- new Debian package, version 2.0. size 1096056 bytes: control archive=1828 bytes. 802 bytes, 19 lines control 2583 bytes, 43 lines md5sums Package: hmmer Version: 3.4+dfsg-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6625 Depends: libc6 (>= 2.38), libdivsufsort3 (>= 2.0.1) Suggests: hmmer-doc (>= 3.4+dfsg-3) Section: science Priority: optional Homepage: http://hmmer.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 2025-09-29 12:45 ./ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/bin/ -rwxr-xr-x root/root 176376 2025-09-29 12:45 ./usr/bin/alimask -rwxr-xr-x root/root 392392 2025-09-29 12:45 ./usr/bin/hmmalign -rwxr-xr-x root/root 380584 2025-09-29 12:45 ./usr/bin/hmmbuild -rwxr-xr-x root/root 187304 2025-09-29 12:45 ./usr/bin/hmmconvert -rwxr-xr-x root/root 216744 2025-09-29 12:45 ./usr/bin/hmmemit -rwxr-xr-x root/root 195656 2025-09-29 12:45 ./usr/bin/hmmfetch -rwxr-xr-x root/root 174984 2025-09-29 12:45 ./usr/bin/hmmlogo -rwxr-xr-x root/root 512360 2025-09-29 12:45 ./usr/bin/hmmpgmd -rwxr-xr-x root/root 516552 2025-09-29 12:45 ./usr/bin/hmmpgmd_shard -rwxr-xr-x root/root 191160 2025-09-29 12:45 ./usr/bin/hmmpress -rwxr-xr-x root/root 447432 2025-09-29 12:45 ./usr/bin/hmmscan -rwxr-xr-x root/root 460040 2025-09-29 12:45 ./usr/bin/hmmsearch -rwxr-xr-x root/root 214520 2025-09-29 12:45 ./usr/bin/hmmsim -rwxr-xr-x root/root 174664 2025-09-29 12:45 ./usr/bin/hmmstat -rwxr-xr-x root/root 550152 2025-09-29 12:45 ./usr/bin/jackhmmer -rwxr-xr-x root/root 216328 2025-09-29 12:45 ./usr/bin/makehmmerdb -rwxr-xr-x root/root 635880 2025-09-29 12:45 ./usr/bin/nhmmer -rwxr-xr-x root/root 472568 2025-09-29 12:45 ./usr/bin/nhmmscan -rwxr-xr-x root/root 487144 2025-09-29 12:45 ./usr/bin/phmmer drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/lib/x86_64-linux-gnu/hmmer/ -rwxr-xr-x root/root 75608 2025-09-29 12:45 ./usr/lib/x86_64-linux-gnu/hmmer/hmmc2 drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/doc/hmmer/ -rw-r--r-- root/root 491 2025-09-29 12:45 ./usr/share/doc/hmmer/README.Debian -rw-r--r-- root/root 981 2025-09-29 12:45 ./usr/share/doc/hmmer/changelog.Debian.gz -rw-r--r-- root/root 5159 2025-09-29 12:45 ./usr/share/doc/hmmer/copyright drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-29 12:45 ./usr/share/man/man1/ -rw-r--r-- root/root 3649 2025-09-29 12:45 ./usr/share/man/man1/alimask.1.gz -rw-r--r-- root/root 1565 2025-09-29 12:45 ./usr/share/man/man1/hmmalign.1.gz -rw-r--r-- root/root 5446 2025-09-29 12:45 ./usr/share/man/man1/hmmbuild.1.gz -rw-r--r-- root/root 987 2025-09-29 12:45 ./usr/share/man/man1/hmmconvert.1.gz -rw-r--r-- root/root 2197 2025-09-29 12:45 ./usr/share/man/man1/hmmemit.1.gz -rw-r--r-- root/root 2204 2025-09-29 12:45 ./usr/share/man/man1/hmmer.1.gz -rw-r--r-- root/root 1779 2025-09-29 12:45 ./usr/share/man/man1/hmmfetch.1.gz -rw-r--r-- root/root 1074 2025-09-29 12:45 ./usr/share/man/man1/hmmlogo.1.gz -rw-r--r-- root/root 2076 2025-09-29 12:45 ./usr/share/man/man1/hmmpgmd.1.gz -rw-r--r-- root/root 1720 2025-09-29 12:45 ./usr/share/man/man1/hmmpgmd_shard.1.gz -rw-r--r-- root/root 917 2025-09-29 12:45 ./usr/share/man/man1/hmmpress.1.gz -rw-r--r-- root/root 4519 2025-09-29 12:45 ./usr/share/man/man1/hmmscan.1.gz -rw-r--r-- root/root 4440 2025-09-29 12:45 ./usr/share/man/man1/hmmsearch.1.gz -rw-r--r-- root/root 5220 2025-09-29 12:45 ./usr/share/man/man1/hmmsim.1.gz -rw-r--r-- root/root 1339 2025-09-29 12:45 ./usr/share/man/man1/hmmstat.1.gz -rw-r--r-- root/root 7566 2025-09-29 12:45 ./usr/share/man/man1/jackhmmer.1.gz -rw-r--r-- root/root 1432 2025-09-29 12:45 ./usr/share/man/man1/makehmmerdb.1.gz -rw-r--r-- root/root 6755 2025-09-29 12:45 ./usr/share/man/man1/nhmmer.1.gz -rw-r--r-- root/root 4868 2025-09-29 12:45 ./usr/share/man/man1/nhmmscan.1.gz -rw-r--r-- root/root 5043 2025-09-29 12:45 ./usr/share/man/man1/phmmer.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 20 Sep 2026 00:03:40 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 20 Sep 2026 00:03:40 +0000 | +------------------------------------------------------------------------------+ Purging /build/hmmer-2ml2gJ Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 20 Sep 2026 00:03:41 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 296192 Build-Time: 664 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 15 Job: /srv/debomatic/incoming/hmmer_3.4+dfsg-3.dsc Machine Architecture: amd64 Package: hmmer Package-Time: 688 Source-Version: 3.4+dfsg-3 Space: 296192 Status: successful Version: 3.4+dfsg-3 -------------------------------------------------------------------------------- Finished at 2026-09-20T00:03:36Z Build needed 00:11:28, 296192k disk space