I: pbuilder: network access will be disabled during build
I: Current time: Fri May 5 18:45:24 +14 2023
I: pbuilder-time-stamp: 1683261924
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [hhsuite_3.3.0+ds-7.dsc]
I: copying [./hhsuite_3.3.0+ds.orig.tar.xz]
I: copying [./hhsuite_3.3.0+ds-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Oct 26 03:36:26 2022 +14
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-7.dsc: no acceptable signature found
dpkg-source: info: extracting hhsuite in hhsuite-3.3.0+ds
dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz
dpkg-source: info: unpacking hhsuite_3.3.0+ds-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying test_without_mpi
dpkg-source: info: applying perlscript_uselib
dpkg-source: info: applying perl_interpreter
dpkg-source: info: applying drop-fmemopen.h.patch
dpkg-source: info: applying python3
dpkg-source: info: applying ppc64el.patch
dpkg-source: info: applying exe_suffix
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D01_modify_environment starting
debug: Running on virt32a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 5 18:46 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4'
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=d4d837000122456ebced6b64d63cbe17
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=7076
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.masyQHVx/pbuilderrc_z6iG --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.masyQHVx/b2 --logfile b2/build.log --extrapackages usrmerge hhsuite_3.3.0+ds-7.dsc'
SUDO_GID=113
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:3142/
I: uname -a
Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 21 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 21 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 21 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 133220 Sep 21 2022 date
-rwxr-xr-x 1 root root 67732 Sep 21 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 21 2022 df
-rwxr-xr-x 1 root root 133632 Sep 21 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 21 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 23 23:51 login
-rwxr-xr-x 1 root root 133632 Sep 21 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 23 23:02 more
-rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount
-rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 21 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 May 5 18:46 sh -> /bin/bash
-rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 21 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 23 23:02 su
-rwxr-xr-x 1 root root 67584 Sep 21 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 21 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 21 2022 true
-rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount
-rwxr-xr-x 1 root root 67572 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19329 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on imagemagick; however:
Package imagemagick is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libaom3{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcurl4{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx265-199{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl ghostscript gsfonts libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libsasl2-modules lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
Need to get 39.8 MB of archives. After unpacking 140 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf libaom3 armhf 3.6.0-1 [1369 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf libdav1d6 armhf 1.0.0-2 [256 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf libde265-0 armhf 1.0.11-1 [143 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf libx265-199 armhf 3.5-2+b1 [580 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf libheif1 armhf 1.15.1-1 [183 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf liblcms2-2 armhf 2.14-2 [125 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.5 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libopenjp2-7 armhf 2.5.0-1+b1 [170 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB]
Get: 23 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.1 [242 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-5 [295 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf libwebpdemux2 armhf 1.2.4-0.1 [98.2 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf libwebpmux3 armhf 1.2.4-0.1 [105 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [165 kB]
Get: 38 http://deb.debian.org/debian bookworm/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [1634 kB]
Get: 39 http://deb.debian.org/debian bookworm/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [402 kB]
Get: 40 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 44 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 46 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 47 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 48 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 49 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 50 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 51 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 52 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 53 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 54 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 55 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 56 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 57 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB]
Get: 58 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB]
Get: 59 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB]
Get: 60 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB]
Get: 61 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB]
Get: 62 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB]
Get: 63 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB]
Get: 64 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB]
Get: 65 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB]
Get: 66 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB]
Get: 67 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB]
Get: 68 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB]
Get: 69 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB]
Get: 70 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB]
Get: 71 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 72 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 73 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 74 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 75 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 76 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 77 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 78 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 79 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 80 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 81 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 82 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 83 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 84 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB]
Get: 85 http://deb.debian.org/debian bookworm/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 86 http://deb.debian.org/debian bookworm/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.6 [338 kB]
Get: 87 http://deb.debian.org/debian bookworm/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.6 [122 kB]
Get: 88 http://deb.debian.org/debian bookworm/main armhf libsimde-dev all 0.7.4~rc2-2 [377 kB]
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Setting up libproc2-0:armhf (2:4.0.2-3) ...
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cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
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[ 9%] Built target hhviterbialgorithm_with_celloff_and_ss
make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src/cs /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src/cs /build/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 9%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp
[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/aa.cc
cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp
[ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_and_ss.a
/build/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)':
/build/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
504 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /build/hhsuite-3.3.0+ds/src/a3m_compress.h:11,
from /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 11%] Built target hhviterbialgorithm_and_ss
make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color=
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cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/as.cc
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make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 13%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c
/build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':
/build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:42: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
/build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:47: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a
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make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend
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cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c
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cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated
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[ 17%] Linking C executable ffindex_reduce
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make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend
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[ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
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/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
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cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c
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make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c
[ 24%] Linking C executable ffindex_from_fasta
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a
[ 25%] Linking C executable ffindex_get
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 25%] Built target ffindex_from_fasta
make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend
[ 25%] Built target ffindex_get
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color=
make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c
[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c
[ 28%] Linking C executable ffindex_unpack
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 28%] Built target ffindex_unpack
make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c
[ 30%] Linking C executable ffindex_modify
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 30%] Built target ffindex_modify
make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c
[ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc
[ 33%] Linking C executable ffindex_order
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a
[ 34%] Linking C executable ffindex_from_fasta_with_split
cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 34%] Built target ffindex_from_fasta_with_split
make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 35%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_extract.cpp
[ 35%] Built target ffindex_order
make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 36%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_reduce.cpp
[ 37%] Linking CXX executable a3m_extract
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 37%] Built target a3m_extract
make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 38%] Linking CXX executable a3m_reduce
[ 39%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 39%] Built target a3m_reduce
make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 40%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp
[ 41%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc
cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp
cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h
[ 42%] Generating ../generated/cs219.lib.h
cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated
[ 43%] Linking CXX executable a3m_database_reduce
cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp
cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 43%] Built target generated
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 44%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 44%] Built target a3m_database_reduce
[ 45%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/log.cc
[ 46%] Linking CXX executable a3m_database_extract
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 46%] Built target a3m_database_extract
[ 47%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/application.cc
[ 48%] Linking CXX executable a3m_database_filter
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 48%] Built target a3m_database_filter
[ 49%] Linking CXX static library libCS_OBJECTS.a
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake
cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o
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[ 49%] Built target CS_OBJECTS
make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o
[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits.cpp
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhdecl.cpp
[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhit.cpp
[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhmatrices.cpp
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhsearch.cpp
[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhalign.cpp
[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhitlist.cpp
[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp
[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhutil.cpp
[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-3.3.0+ds/src/util.cpp
In file included from /usr/include/c++/12/vector:70,
from /build/hhsuite-3.3.0+ds/src/hhhit.h:14,
from /build/hhsuite-3.3.0+ds/src/hhhitlist.h:16,
from /build/hhsuite-3.3.0+ds/src/hhhitlist.cpp:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void HitList::PrintMatrices(HMM*, std::stringstream&, bool, size_t, const float (*)[20])' at /build/hhsuite-3.3.0+ds/src/hhhitlist.cpp:591:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhalignment.cpp
[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp
[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhmm.cpp
[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp
[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfullalignment.cpp
/build/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])':
/build/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=]
1797 | sprintf(details, "The alingment %s does not contain any sequences.",
| ^~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /build/hhsuite-3.3.0+ds/src/hhalignment.h:6,
from /build/hhsuite-3.3.0+ds/src/hhalignment.cpp:8:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /build/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp
[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp
[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbi.cpp
[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp
[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp
[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp
[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp
[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp
[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp
[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhdatabase.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /build/hhsuite-3.3.0+ds/lib/simd/simd.h:9,
from /build/hhsuite-3.3.0+ds/src/util.h:23,
from /build/hhsuite-3.3.0+ds/src/hhhmm.h:8,
from /build/hhsuite-3.3.0+ds/src/hhprefilter.h:17,
from /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:8:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Distance = int; _Tp = pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp
[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp
In file included from /usr/include/c++/12/vector:70,
from /build/hhsuite-3.3.0+ds/src/hhprefilter.h:11:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<double, int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from '_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:531:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /build/hhsuite-3.3.0+ds/src/util.h:20,
from /build/hhsuite-3.3.0+ds/src/hhhmm.h:8,
from /build/hhsuite-3.3.0+ds/src/hhhmmsimd.h:5,
from /build/hhsuite-3.3.0+ds/src/hhviterbirunner.h:4,
from /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void ViterbiConsumerThread::align(int, int, float, char)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:67:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void ViterbiRunner::merge_thread_results(std::vector<Hit>&, std::vector<HHEntry*>&, std::map<std::__cxx11::basic_string<char>, std::vector<Viterbi::BacktraceResult> >&, std::vector<ViterbiConsumerThread*>&, int, float)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:259:31,
inlined from 'std::vector<Hit> ViterbiRunner::alignment(Parameters&, HMMSimd*, std::vector<HHEntry*>, float, float*, const float (*)[20], const float (*)[20], const float (*)[20], int, const float (*)[4][11], const float (*)[11][4][11], const float (*)[11][8])' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:173:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void ViterbiRunner::merge_thread_results(std::vector<Hit>&, std::vector<HHEntry*>&, std::map<std::__cxx11::basic_string<char>, std::vector<Viterbi::BacktraceResult> >&, std::vector<ViterbiConsumerThread*>&, int, float)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:259:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfunc.cpp
[ 79%] Linking CXX static library libHH_OBJECTS.a
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
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cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
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[ 95%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /build/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 96%] Linking CXX executable hhblits_omp
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 96%] Built target hhblits_omp
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build
make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /build/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 98%] Linking CXX executable hhsearch_omp
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 98%] Built target hhsearch_omp
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /build/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 99%] Linking CXX executable hhalign_omp
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[ 99%] Built target hhalign_omp
/build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)':
/build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /build/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15,
inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable hhblits_ca3m
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[100%] Built target hhblits_ca3m
[100%] Linking CXX executable cstranslate
cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
[100%] Built target cstranslate
make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0
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debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
dh_auto_build --builddirectory mybuild/data
cd mybuild/data && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks
cd /build/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all
make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
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cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/data /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake --color=
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[100%] Built target generated
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debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
cd /build/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-3.3.0+ds/mybuild/src:/build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh
- 18:53:41.883 INFO: query.a3m is in A2M, A3M or FASTA format
- 18:53:43.345 INFO: Alternative alignment: 0
- 18:53:43.545 INFO: 1 alignments done
- 18:53:43.684 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 118
Neff 4.29223
Searched_HMMs 1
Date Fri May 5 18:53:44 2023
Command hhalign -i query.a3m -o result.hhr -t query.a3m
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431)
query.a3m 0 32127 1257 0
query.a3m 0 32666 9 0
query.a3m 0 32666 313 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 18:53:48.870 INFO: Searching 1 column state sequences.
- 18:53:49.077 INFO: query.a3m is in A2M, A3M or FASTA format
- 18:53:49.164 INFO: Iteration 1
- 18:53:50.403 INFO: Prefiltering database
- 18:53:51.640 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 18:53:51.651 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 18:53:51.651 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 18:53:51.651 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 18:53:51.851 INFO: Alternative alignment: 0
- 18:53:52.050 INFO: 1 alignments done
- 18:53:52.051 INFO: Alternative alignment: 1
- 18:53:52.243 INFO: 1 alignments done
- 18:53:52.243 INFO: Alternative alignment: 2
- 18:53:52.243 INFO: Alternative alignment: 3
- 18:53:53.727 INFO: Premerge done
- 18:53:53.727 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 18:53:53.883 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 59 out of 118
Neff 4.27431
Searched_HMMs 1
Date Fri May 5 18:53:53 2023
Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431)
- 18:53:53.972 INFO: Searching 1 column state sequences.
- 18:53:54.145 INFO: Thread 0 query.a3m
- 18:53:54.196 INFO: query.a3m is in A2M, A3M or FASTA format
- 18:53:54.281 INFO: Iteration 1
- 18:53:56.561 INFO: Prefiltering database
- 18:53:58.854 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 18:53:58.864 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 18:53:58.864 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 18:53:58.864 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 18:53:58.962 INFO: Alternative alignment: 0
- 18:53:59.161 INFO: 1 alignments done
- 18:53:59.161 INFO: Alternative alignment: 1
- 18:53:59.353 INFO: 1 alignments done
- 18:53:59.353 INFO: Alternative alignment: 2
- 18:53:59.353 INFO: Alternative alignment: 3
- 18:54:01.836 INFO: Premerge done
- 18:54:01.836 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 18:54:01.959 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
- 18:54:02.247 INFO: query.a3m is in A2M, A3M or FASTA format
- 18:54:02.332 INFO: Searching 1 database HHMs without prefiltering
- 18:54:02.332 INFO: Iteration 1
- 18:54:03.506 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 18:54:03.699 INFO: Alternative alignment: 0
- 18:54:03.892 INFO: 1 alignments done
- 18:54:03.892 INFO: Alternative alignment: 1
- 18:54:04.080 INFO: 1 alignments done
- 18:54:04.080 INFO: Alternative alignment: 2
- 18:54:04.080 INFO: Alternative alignment: 3
- 18:54:05.627 INFO: Premerge done
- 18:54:05.627 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 18:54:05.787 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 118
Neff 4.29223
Searched_HMMs 1
Date Fri May 5 18:54:05 2023
Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431)
- 18:54:06.045 INFO: Thread 0 query.a3m
- 18:54:06.095 INFO: query.a3m is in A2M, A3M or FASTA format
- 18:54:06.179 INFO: Searching 1 database HHMs without prefiltering
- 18:54:06.180 INFO: Iteration 1
- 18:54:08.508 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 18:54:08.606 INFO: Alternative alignment: 0
- 18:54:08.799 INFO: 1 alignments done
- 18:54:08.799 INFO: Alternative alignment: 1
- 18:54:08.985 INFO: 1 alignments done
- 18:54:08.985 INFO: Alternative alignment: 2
- 18:54:08.985 INFO: Alternative alignment: 3
- 18:54:11.471 INFO: Premerge done
- 18:54:11.471 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 18:54:11.588 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
mkdir -p /build/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin
dh_auto_install --builddirectory mybuild
cd mybuild && make -j4 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl
-- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl
make[2]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done
dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin
dh_install -phhsuite usr/bin/ffindex_* usr/bin/
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
debian/rules override_dh_auto_install-indep
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
dh_auto_install --builddirectory mybuild/data
cd mybuild/data && make -j4 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data'
cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
cd /build/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall
make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild'
make[3]: Nothing to be done for 'data/preinstall'.
make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin
-- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq
make[2]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild/data'
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman-arch
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1'
dh_installman --arch
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
dh_installman -Nhhsuite
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
dh_fixperms
chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
dh_fixperms -Nhhsuite
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhfilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhmake contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_ca3m contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb
debian/rules override_dh_gencontrol
make[1]: Entering directory '/build/hhsuite-3.3.0+ds'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), "
make[1]: Leaving directory '/build/hhsuite-3.3.0+ds'
dh_md5sums
dh_builddeb
dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-7_armhf.deb'.
dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-7_armhf.deb'.
dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-7_all.deb'.
dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-7_armhf.buildinfo
dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-7_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/7076/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/7076 and its subdirectories
I: Current time: Fri May 5 18:59:06 +14 2023
I: pbuilder-time-stamp: 1683262746