I: pbuilder: network access will be disabled during build
I: Current time: Fri Jun 11 01:24:58 -12 2021
I: pbuilder-time-stamp: 1623417898
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
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: using eatmydata during job
I: Copying source file
I: copying [fsa_1.15.9+dfsg-6.dsc]
I: copying [./fsa_1.15.9+dfsg.orig.tar.xz]
I: copying [./fsa_1.15.9+dfsg-6.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.xUWUJCKF/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 15 05:07:02 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fsa_1.15.9+dfsg-6.dsc
dpkg-source: info: extracting fsa in fsa-1.15.9+dfsg
dpkg-source: info: unpacking fsa_1.15.9+dfsg.orig.tar.xz
dpkg-source: info: unpacking fsa_1.15.9+dfsg-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no-display.patch
dpkg-source: info: applying removed-pdf-only-docs.patch
dpkg-source: info: applying privacy_breach_logo.patch
dpkg-source: info: applying fixed-check-for-m64-flag.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/12068/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='443b36d745c14dab941c17ee6961058d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='12068'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DJMweHCn8Q/pbuilderrc_fspz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DJMweHCn8Q/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos2-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux
I: ls -l /bin
total 5776
-rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 38824 Sep 22 2020 cat
-rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp
-rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod
-rwxr-xr-x 1 root root 75752 Sep 22 2020 chown
-rwxr-xr-x 1 root root 157960 Sep 22 2020 cp
-rwxr-xr-x 1 root root 128724 Dec 10 2020 dash
-rwxr-xr-x 1 root root 124904 Sep 22 2020 date
-rwxr-xr-x 1 root root 92172 Sep 22 2020 dd
-rwxr-xr-x 1 root root 100752 Sep 22 2020 df
-rwxr-xr-x 1 root root 153964 Sep 22 2020 dir
-rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 34664 Sep 22 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 34664 Sep 22 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt
-rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount
-rwxr-xr-x 1 root root 210488 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
-rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip
-rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 83980 Sep 22 2020 ln
-rwxr-xr-x 1 root root 55572 Feb 7 2020 login
-rwxr-xr-x 1 root root 153964 Sep 22 2020 ls
-rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk
-rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir
-rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod
-rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp
-rwxr-xr-x 1 root root 58920 Feb 7 02:38 more
-rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount
-rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint
-rwxr-xr-x 1 root root 157996 Sep 22 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd
lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash
-rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink
-rwxr-xr-x 1 root root 75720 Sep 22 2020 rm
-rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir
-rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 125036 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jun 9 22:32 sh -> dash
-rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep
-rwxr-xr-x 1 root root 83880 Sep 22 2020 stty
-rwsr-xr-x 1 root root 79396 Feb 7 02:38 su
-rwxr-xr-x 1 root root 34696 Sep 22 2020 sync
-rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar
-rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 108520 Sep 22 2020 touch
-rwxr-xr-x 1 root root 34664 Sep 22 2020 true
-rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount
-rwxr-xr-x 1 root root 34664 Sep 22 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
-rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir
-rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
-rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
I: user script /srv/workspace/pbuilder/12068/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: i386
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), mummer, exonerate, 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 ... 19675 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 mummer; however:
Package mummer is not installed.
pbuilder-satisfydepends-dummy depends on exonerate; however:
Package exonerate 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} exonerate{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mummer{a} po-debconf{a} readline-common{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs
0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.5 MB of archives. After unpacking 88.6 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB]
Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB]
Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB]
Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB]
Get: 6 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB]
Get: 7 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB]
Get: 8 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB]
Get: 9 http://deb.debian.org/debian bullseye/main i386 gawk i386 1:5.1.0-1 [618 kB]
Get: 10 http://deb.debian.org/debian bullseye/main i386 liblocale-gettext-perl i386 1.07-4+b1 [19.4 kB]
Get: 11 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB]
Get: 12 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB]
Get: 13 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB]
Get: 14 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB]
Get: 15 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB]
Get: 16 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB]
Get: 17 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB]
Get: 18 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 19 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB]
Get: 20 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB]
Get: 21 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB]
Get: 22 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB]
Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 24 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 25 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 26 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get: 27 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get: 28 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB]
Get: 29 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB]
Get: 30 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB]
Get: 31 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB]
Get: 32 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB]
Get: 33 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 34 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 35 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB]
Get: 36 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB]
Get: 37 http://deb.debian.org/debian bullseye/main i386 exonerate i386 2.4.0-5 [1749 kB]
Get: 38 http://deb.debian.org/debian bullseye/main i386 help2man i386 1.48.1 [190 kB]
Get: 39 http://deb.debian.org/debian bullseye/main i386 mummer i386 3.23+dfsg-7 [670 kB]
Fetched 23.5 MB in 6s (4217 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
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(Reading database ... 19675 files and directories currently installed.)
Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../3-libpipeline1_1.5.3-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../4-man-db_2.9.4-2_i386.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../5-readline-common_8.1-1_all.deb ...
Unpacking readline-common (8.1-1) ...
Selecting previously unselected package libreadline8:i386.
Preparing to unpack .../6-libreadline8_8.1-1_i386.deb ...
Unpacking libreadline8:i386 (8.1-1) ...
Selecting previously unselected package libsigsegv2:i386.
Preparing to unpack .../7-libsigsegv2_2.13-1_i386.deb ...
Unpacking libsigsegv2:i386 (2.13-1) ...
Setting up readline-common (8.1-1) ...
Setting up libreadline8:i386 (8.1-1) ...
Setting up libsigsegv2:i386 (2.13-1) ...
Selecting previously unselected package gawk.
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(Reading database ... 20281 files and directories currently installed.)
Preparing to unpack .../00-gawk_1%3a5.1.0-1_i386.deb ...
Unpacking gawk (1:5.1.0-1) ...
Selecting previously unselected package liblocale-gettext-perl.
Preparing to unpack .../01-liblocale-gettext-perl_1.07-4+b1_i386.deb ...
Unpacking liblocale-gettext-perl (1.07-4+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../02-sensible-utils_0.0.14_all.deb ...
Unpacking sensible-utils (0.0.14) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../03-libmagic-mgc_1%3a5.39-3_i386.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../04-libmagic1_1%3a5.39-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../05-file_1%3a5.39-3_i386.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../06-gettext-base_0.21-4_i386.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package m4.
Preparing to unpack .../07-m4_1.4.18-5_i386.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../08-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../09-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../11-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../12-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../13-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../14-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../15-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../16-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../17-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../18-dh-strip-nondeterminism_1.11.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.11.0-1) ...
Selecting previously unselected package libelf1:i386.
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Unpacking libelf1:i386 (0.183-1) ...
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Unpacking libicu67:i386 (67.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../22-libxml2_2.9.10+dfsg-6.7_i386.deb ...
Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ...
Selecting previously unselected package gettext.
Preparing to unpack .../23-gettext_0.21-4_i386.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.31-12) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/fsa-1.15.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package fsa
dpkg-buildpackage: info: source version 1.15.9+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_clean
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
dh_auto_configure
./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1111' is supported by ustar format... yes
checking whether GID '1111' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for gawk... (cached) gawk
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for unsigned long long int... yes
checking for uintmax_t... yes
checking for ptrdiff_t... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for floor... yes
checking for memmove... yes
checking for pow... yes
checking for regcomp... yes
checking for sqrt... yes
checking for strchr... yes
checking for strcspn... yes
checking for strspn... yes
checking for strstr... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for mummer... /usr/bin/mummer
checking for exonerate... /usr/bin/exonerate
checking for struct sysinfo.totalram... yes
checking for struct sysinfo.mem_unit... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking for javac... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/main/Makefile
config.status: creating src/manager/Makefile
config.status: creating src/fsa/Makefile
config.status: creating src/annealing/Makefile
config.status: creating src/math/Makefile
config.status: creating src/util/Makefile
config.status: creating src/seq/Makefile
config.status: creating perl/Makefile
config.status: creating examples/Makefile
config.status: creating html/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- FSA 1.15.9 Configuration Results --
C++ compiler: g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG
GCC version: gcc (Debian 10.2.1-6) 10.2.1 20210110
Host System type: i686-pc-linux-gnu
Install prefix: /usr
See config.h for further configuration information.
Email <fsa@math.berkeley.edu> with questions and bug reports.
dh_auto_build
make -j10
make[1]: Entering directory '/build/fsa-1.15.9+dfsg'
make all-recursive
make[2]: Entering directory '/build/fsa-1.15.9+dfsg'
Making all in src/util
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/util'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dexception.o dexception.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o logfile.o logfile.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o memcheck.o memcheck.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o misc.o misc.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o opts_list.o opts_list.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o regexp.o regexp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sstring.o sstring.cc
opts_list.cc:99:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
99 | SET_VERSION_INFO(*this);
| ^
In file included from opts_list.cc:2:
../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n";
| ^~~~~~~~
opts_list.cc:99:3: note: in expansion of macro 'SET_VERSION_INFO'
99 | SET_VERSION_INFO(*this);
| ^~~~~~~~~~~~~~~~
rm -f libutil.a
ar cru libutil.a dexception.o logfile.o memcheck.o misc.o opts_list.o regexp.o sstring.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libutil.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util'
Making all in src/math
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/math'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mathematics.o mathematics.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mst.o mst.cc
rm -f libmath.a
ar cru libmath.a mathematics.o mst.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmath.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math'
Making all in src/seq
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment.o alignment.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gff.o gff.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mercator.o mercator.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc
rm -f libseq.a
ar cru libseq.a alphabet.o alignment.o gff.o mercator.o sequence.o similarity_matrix.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq'
Making all in src/manager
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o manager.o manager.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mw_adapter.o mw_adapter.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_adapter.o db_adapter.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_misc.o db_misc.cc
In file included from ../../src/fsa/anchors.h:17,
from ../../src/fsa/fsa.h:71,
from db_misc.cc:7:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/manager/manager.h:12,
from manager.cc:6:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
rm -f libmanager.a
ar cru libmanager.a manager.o mw_adapter.o db_adapter.o db_misc.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmanager.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager'
Making all in src/fsa
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o algebras.o algebras.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoacid_indel2dp.o aminoacid_indel2dp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoaciddp.o aminoaciddp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o anchors.o anchors.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o fsa.o fsa.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc
fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] <sequence file(s)>", "Distance-based alignment of DNA, RNA and proteins.");
| ^
In file included from ../../src/fsa/fsa.h:66,
from fsa.cc:11:
../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n";
| ^~~~~~~~
../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO'
152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS);
| ^~~~~~~~~~~~~~~~
fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST'
25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] <sequence file(s)>", "Distance-based alignment of DNA, RNA and proteins.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> Forward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
768 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> Backward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1230 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> Forward(NucleotideAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
768 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1448 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> Forward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
768 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> Backward(NucleotideAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1166 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1979 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1352 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> Forward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
768 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> Backward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1256 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1819 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1472 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> Backward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1320 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
2029 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
1568 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
2189 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
In file included from ../../src/fsa/anchors.h:17,
from ../../src/fsa/fsa.h:71,
from fsa.cc:11:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/fsa/anchors.h:17,
from anchors.cc:16:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/fsa/model.h:32,
from model.cc:8:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const string&, const string&, int) const':
anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const string&, const string&, size_t) const':
anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
rm -f libfsa.a
ar cru libfsa.a algebras.o aminoacid_indel2dp.o aminoaciddp.o anchors.o constraints.o fsa.o model.o nucleotide_indel2dp.o nucleotidedp.o sequence_pair_selector.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfsa.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa'
Making all in src/annealing
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment_DAG.o alignment_DAG.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dotplot.o dotplot.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o tree_weights.o tree_weights.cc
In file included from ../../src/annealing/alignment_DAG.h:58,
from alignment_DAG.cc:12:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
rm -f libannealing.a
ar cru libannealing.a alignment_DAG.o dotplot.o tree_weights.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libannealing.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing'
Making all in src/main
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/main'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o main.o main.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gapcleaner.o gapcleaner.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_coords.o map_coords.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc
In file included from /usr/include/c++/10/ext/hash_map:60,
from ../../src/fsa/dptables.h:43,
from ../../src/fsa/mybanding.h:25,
from ../../src/fsa/model.h:24,
from ../../src/fsa/anchors.h:20,
from ../../src/fsa/fsa.h:71,
from main.cc:8:
/usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
In file included from ../../src/annealing/alignment_DAG.h:58,
from gapcleaner.cc:11:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/fsa/anchors.h:17,
from ../../src/fsa/fsa.h:71,
from main.cc:8:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o percentid percentid.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o prot2codon prot2codon.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta slice_fasta.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta_gff slice_fasta_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_mercator_alignment slice_mercator_alignment.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_coords map_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main'
Making all in perl
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/perl'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/perl'
Making all in examples
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/examples'
Making all in html
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/html'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/html'
Making all in tests
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/tests'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg'
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg'
make[1]: Leaving directory '/build/fsa-1.15.9+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/fsa-1.15.9+dfsg'
echo "Tests seem to miss some files:"
Tests seem to miss some files:
echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop."
make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop.
make[1]: Leaving directory '/build/fsa-1.15.9+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j10 install DESTDIR=/build/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/fsa-1.15.9+dfsg'
Making install in src/util
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/util'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/util'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util'
Making install in src/math
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/math'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/math'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math'
Making install in src/seq
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq'
Making install in src/manager
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager'
Making install in src/fsa
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa'
Making install in src/annealing
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing'
Making install in src/main
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/main'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/main'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/fsa-1.15.9+dfsg/debian/fsa/usr/bin'
/usr/bin/install -c fsa gapcleaner isect_mercator_alignment_gff map_coords map_gff_coords percentid prot2codon slice_fasta slice_fasta_gff slice_mercator_alignment translate '/build/fsa-1.15.9+dfsg/debian/fsa/usr/bin'
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main'
Making install in perl
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/perl'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/perl'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/perl'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/perl'
Making install in examples
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/examples'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/examples'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/examples'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/examples'
Making install in html
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/html'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/html'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/html'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/html'
Making install in tests
make[2]: Entering directory '/build/fsa-1.15.9+dfsg/tests'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/tests'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/tests'
make[2]: Entering directory '/build/fsa-1.15.9+dfsg'
make[3]: Entering directory '/build/fsa-1.15.9+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/fsa-1.15.9+dfsg'
make[2]: Leaving directory '/build/fsa-1.15.9+dfsg'
make[1]: Leaving directory '/build/fsa-1.15.9+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/fsa-1.15.9+dfsg'
dh_install
mv /build/fsa-1.15.9+dfsg/debian/fsa/usr/bin/translate /build/fsa-1.15.9+dfsg/debian/fsa/usr/bin/fsa-translate
make[1]: Leaving directory '/build/fsa-1.15.9+dfsg'
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_i386.deb'.
dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-6_i386.deb'.
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../fsa_1.15.9+dfsg-6_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
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/12068 and its subdirectories
I: Current time: Fri Jun 11 01:32:52 -12 2021
I: pbuilder-time-stamp: 1623418372