I: pbuilder: network access will be disabled during build
I: Current time: Wed Apr 12 23:22:35 -12 2023
I: pbuilder-time-stamp: 1681384955
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: using eatmydata during job
I: Copying source file
I: copying [mafft_7.505-1.dsc]
I: copying [./mafft_7.505.orig.tar.gz]
I: copying [./mafft_7.505-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Jun 25 07:18:48 2022 -12
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./mafft_7.505-1.dsc: no acceptable signature found
dpkg-source: info: extracting mafft in mafft-7.505
dpkg-source: info: unpacking mafft_7.505.orig.tar.gz
dpkg-source: info: unpacking mafft_7.505-1.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/28466/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 parallel=8'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='c96ea8da3d7e4bd5b9c89d92d78007f2'
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='28466'
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/r-b-build.0A6yFn7c/pbuilderrc_vPKj --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0A6yFn7c/b1 --logfile b1/build.log mafft_7.505-1.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 ionos12-i386 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux
I: ls -l /bin
total 6040
-rwxr-xr-x 1 root root 1408088 Feb 12 08:21 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 23:43 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 22:20 more
-rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount
-rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Dec 18 05:00 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 08:21 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 04:31 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 22:20 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 602584 Feb 16 2021 tar
-rwxr-xr-x 1 root root 13860 Nov 2 04:31 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/28466/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)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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.
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} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.0 MB of archives. After unpacking 72.7 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Fetched 19.0 MB in 0s (49.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 45%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19604 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_i386.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-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 .../19-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:i386.
Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ...
Unpacking libelf1:i386 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_i386.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../24-libicu72_72.1-3_i386.deb ...
Unpacking libicu72:i386 (72.1-3) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_i386.deb ...
Unpacking libxml2:i386 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_i386.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Setting up libpipeline1:i386 (1.5.7-1) ...
Setting up libicu72:i386 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:i386 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:i386 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:i386 (0.188-2.1) ...
Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-8) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/mafft-7.505/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mafft_7.505-1_source.changes
dpkg-buildpackage: info: source package mafft
dpkg-buildpackage: info: source version 7.505-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --sourcedirectory=core
dh_auto_clean -O--sourcedirectory=core
cd core && make -j8 clean
make[1]: Entering directory '/build/mafft-7.505/core'
rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno
make[1]: Leaving directory '/build/mafft-7.505/core'
dh_autoreconf_clean -O--sourcedirectory=core
debian/rules override_dh_clean
make[1]: Entering directory '/build/mafft-7.505'
rm -rf binaries/* scripts/*
dh_clean
make[1]: Leaving directory '/build/mafft-7.505'
debian/rules binary
dh binary --sourcedirectory=core
dh_update_autotools_config -O--sourcedirectory=core
dh_autoreconf -O--sourcedirectory=core
dh_auto_configure -O--sourcedirectory=core
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/mafft-7.505'
dh_auto_build -- \
PREFIX=/usr/lib/mafft \
ENABLE_MULTITHREAD=-Denablemultithread \
LIBDIR=/usr/lib/mafft/lib/mafft \
CFLAGS="-g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \
LDFLAGS="-Wl,-z,relro -Wl,-z,now"
cd core && make -j8 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/mafft-7.505/core'
cp mafftash_premafft.tmpl mafftash_premafft.pl
cp seekquencer_premafft.tmpl seekquencer_premafft.pl
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c
io.c: In function 'PreRead':
io.c:1120:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1120 | fgets( b, B-1, fp ); *locnjob = atoi( b );
| ^~~~~~~~~~~~~~~~~~~
io.c:1125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1125 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:1129:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1129 | fgets( b, B-1, fp ); nleni = atoi( b );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'FRead':
io.c:1165:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1165 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:1255:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1255 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_part_pointer':
io.c:2707:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2707 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2709:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2709 | fgets( b, B, fp ); nseq0 = atoi( b ); // 2020/Oct/23
| ^~~~~~~~~~~~~~~~~
io.c:2715:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2715 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_pointer':
io.c:2745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2745 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2746:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2746 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 )
| ^~~~~~~~~~~~~~~~~
io.c:2751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2751 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf':
io.c:2779:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2779 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2780 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
| ^~~~~~~~~~~~~~~~~
io.c:2781:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2781 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_double':
io.c:2809:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2809 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2810:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2810 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
| ^~~~~~~~~~~~~~~~~
io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2811 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_int':
io.c:2839:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2839 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2840 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
| ^~~~~~~~~~~~~~~~~
io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2841 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_pointer':
io.c:2870:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2870 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2871 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
| ^~~~~~~~~~~~~~~~~
io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2872 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2':
io.c:2900:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2900 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2901 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
| ^~~~~~~~~~~~~~~~~
io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2902 | fgets( b, B, fp );
| ^~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta_sub':
io.c:3102:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3102 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3117:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3117 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadSsearch':
io.c:3136:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3136 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_avscore':
io.c:3264:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3264 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3271:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3271 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3272:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3272 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_scoreonly':
io.c:3387:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3387 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3394:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3394 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3395:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3395 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7':
io.c:3505:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3505 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3512:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3512 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3513:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3513 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34noalign':
io.c:3537:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3537 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_nuc':
io.c:3574:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3574 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3600:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3600 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10':
io.c:3713:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3713 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:3737:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3737 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nucbk':
io.c:3840:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3840 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nuc':
io.c:3890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3890 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly':
io.c:3951:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
3951 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34':
io.c:4007:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4007 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c:4033:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4033 | fgets( b, B-1, fp ); // initn:
| ^~~~~~~~~~~~~~~~~~~
io.c:4036:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4036 | fgets( b, B-1, fp ); // Smith-Waterman score
| ^~~~~~~~~~~~~~~~~~~
io.c:4048:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4048 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta3':
io.c:4070:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4070 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta':
io.c:4095:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4095 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt':
io.c:4132:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4132 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt2':
io.c:4153:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4153 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readOtherOptions':
io.c:4249:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
4249 | fgets( b, B-1, fp );
| ^~~~~~~~~~~~~~~~~~~
io.c: In function 'loadaamtx':
io.c:5507:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5507 | fgets( inorder, 999, mf );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5539:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5539 | fgets( line, 999, mf );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5562:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5562 | fgets( line, 999, mf );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readsubalignmentstable':
io.c:5718:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5718 | fgets( line, linelen-1, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5739:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5739 | fgets( line, linelen-1, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readmccaskill':
io.c:5793:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5793 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5803:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5803 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readpairfoldalign':
io.c:5862:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5862 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5875:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5875 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5882:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5882 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5896:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5896 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:5902:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
5902 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readexternalanchors':
io.c:6340:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
6340 | fgets( buf, 9999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from constants.c:7:
blosum.c: In function 'overridematrix':
blosum.c:370:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
370 | fgets( buf, 499, fp );
| ^~~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'check_guidetreefile':
mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
2850 | fgets( string, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek':
mltaln9.c:15685:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15685 | fread( &size, sizeof( int ), 1, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15686:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15686 | fread( &opt, sizeof( double ), 1, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15689 | fread( m, size*sizeof( int ), 3, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15725:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15725 | fread( &c, sizeof( char ), 1, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'check_guidetreefile':
mltaln9.c:2850:9: warning: 'fgets' writing 999 bytes into a region of size 100 overflows the destination [-Wstringop-overflow=]
2850 | fgets( string, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:2834:14: note: destination object 'string' of size 100
2834 | char string[100];
| ^~~~~~
In file included from /usr/include/stdio.h:906,
from mltaln.h:12,
from mltaln9.c:1:
/usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
| ^~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c
rna.c: In function 'rnaalifoldcall':
rna.c:225:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
225 | system( cmd );
| ^~~~~~~~~~~~~
rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
245 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
285 | system( cmd );
| ^~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c
mltaln9.c: In function 'createchain':
mltaln9.c:2113:31: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2113 | instanttree = calloc( treelen, sizeof( char ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mltaln.h:13:
/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
mltaln9.c:2124:17: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2124 | order = calloc( nseq, sizeof( int ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
In function 'fgets',
inlined from 'check_guidetreefile' at mltaln9.c:2850:2:
/usr/include/i386-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
215 | return __fgets_chk_warn (__s, sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c
dvtditr.c: In function 'main':
dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1020 | system( "cp infile.tree GuideTree" ); // tekitou
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave':
mltaln9.c:6494:28: warning: argument 2 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
6494 | int *mem = calloc( sizeof( int ), nseq );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c
dndblast.c: In function 'main':
dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
201 | system( com );
| ^~~~~~~~~~~~~
dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
382 | system( com );
| ^~~~~~~~~~~~~
dndfast7.c: In function 'main':
dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
326 | system( com );
| ^~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c
pairash.c: In function 'prepareash':
pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
639 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
681 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash':
pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
485 | system( com );
| ^~~~~~~~~~~~~
pairash.c: In function 'readrash':
pairash.c:277:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
277 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
284 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
289 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
294 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign':
pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
576 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
587 | system( command );
| ^~~~~~~~~~~~~~~~~
pairash.c: In function 'checkcbeta':
pairash.c:321:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
321 | fgets( linec, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign':
pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
347 | system( com );
| ^~~~~~~~~~~~~
pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
356 | fgets( com, 100, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'readtmalign':
pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
228 | fgets( line, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
232 | fgets( line, nlenmax*2, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
235 | fgets( line, nlenmax*2, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
238 | fgets( line, nlenmax*2, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calllast_once':
pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1056 | system( command );
| ^~~~~~~~~~~~~~~~~
pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1092 | system( command );
| ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx':
pairlocalalign.c:608:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
608 | fgets( gett, 9999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calllast_fast':
pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
981 | system( command );
| ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'lastcallthread':
pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
872 | system( command );
| ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx_singleq':
pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
374 | fgets( gett, 9999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readhat4':
pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1532 | fgets( oneline, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1544 | fgets( oneline, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'recalllara':
pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1245 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'callmxscarna_giving_bpp':
pairlocalalign.c:1408:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1408 | system( com );
| ^~~~~~~~~~~~~
pairlocalalign.c:1410:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1410 | system( com );
| ^~~~~~~~~~~~~
pairlocalalign.c:1430:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1430 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1451:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1451 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1465:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1465 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1485:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1485 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1487:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1487 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calldafs_giving_bpp':
pairlocalalign.c:1291:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1291 | system( com );
| ^~~~~~~~~~~~~
pairlocalalign.c:1293:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1293 | system( com );
| ^~~~~~~~~~~~~
pairlocalalign.c:1313:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1313 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1334:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1334 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1344:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
1344 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
pairlocalalign.c:1364:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1364 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1366:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1366 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1368 | fgets( com, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairalign_node':
pairlocalalign.c:3467:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
3467 | system( "rm -rf hat3dir" ); // toriaezu
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3468:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
3468 | system( "mkdir hat3dir" ); // toriaezu
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
3473 | system( fn );
| ^~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c
pairash.c: In function 'callrash.constprop':
pairash.c:428:43: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 );
| ^
In file included from /usr/include/stdio.h:906,
from mltaln.h:12,
from pairash.c:1:
In function 'sprintf',
inlined from 'callrash.constprop' at pairash.c:428:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash.constprop':
pairash.c:484:36: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=]
484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid );
| ^~ ~~~~~~~~~
In function 'sprintf',
inlined from 'callrash.constprop' at pairash.c:484:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
pairash.c: In function 'calltmalign.constprop':
pairash.c:346:41: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=]
346 | sprintf( com, "mkdir -p %s", cachedir );
| ^~ ~~~~~~~~
In function 'sprintf',
inlined from 'calltmalign.constprop' at pairash.c:346:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign.constprop':
pairash.c:349:45: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
| ^
In function 'sprintf',
inlined from 'calltmalign.constprop' at pairash.c:349:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
maffttext2hex.c: In function 'main':
maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
55 | fgets( (char *)buf, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c
splittbfast.c: In function 'main':
splittbfast.c:3218:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
3218 | system( com );
| ^~~~~~~~~~~~~
tbfast.c: In function 'main':
tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
3254 | system( "cp infile.tree GuideTree" ); // tekitou
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c: In function 'disttbfast':
disttbfast.c:4583:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
4583 | system( "cp infile.tree GuideTree" ); // tekitou
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c
f2cl.c: In function 'main':
f2cl.c:287:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
287 | fgets( gett, B-1, orderfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c
mccaskillwrap.c: In function 'main':
mccaskillwrap.c:372:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mccaskillwrap.c: In function 'athread':
mccaskillwrap.c:115:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
115 | system( com );
| ^~~~~~~~~~~~~
mccaskillwrap.c:117:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
117 | system( com );
| ^~~~~~~~~~~~~
mccaskillwrap.c:129:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
129 | system( com ); // for cygwin, wakaran
| ^~~~~~~~~~~~~
mccaskillwrap.c:155:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
155 | system( com );
| ^~~~~~~~~~~~~
mccaskillwrap.c: In function 'readrawmccaskill':
mccaskillwrap.c:46:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
46 | fgets( gett, 999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c
contrafoldwrap.c: In function 'readcontrafold':
contrafoldwrap.c:57:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
57 | fgets( gett, 9999, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c
regtable2seq.c: In function 'readereg':
regtable2seq.c:69:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
69 | fgets( gett, 999, regfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c:97:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
97 | fgets( gett, 999, regfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c: In function 'readreg':
regtable2seq.c:120:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
120 | fgets( gett, 999, regfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c
gcc -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c
restoreu.c: In function 'main':
restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
185 | fgets( gett, 999, dlfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c
gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft
setdirection.c: In function 'main':
setdirection.c:132:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
132 | fgets( line, 99, difp );
| ^~~~~~~~~~~~~~~~~~~~~~~
sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb
sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
make[2]: Leaving directory '/build/mafft-7.505/core'
make[1]: Leaving directory '/build/mafft-7.505'
dh_auto_test -O--sourcedirectory=core
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=core
dh_prep -O--sourcedirectory=core
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/mafft-7.505'
dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft
cd core && make -j8 install DESTDIR=/build/mafft-7.505/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft
make[2]: Entering directory '/build/mafft-7.505/core'
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
mkdir -p /build/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft
chmod 755 /build/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft
mkdir -p /build/mafft-7.505/debian/mafft/usr/lib/mafft/bin
chmod 755 /build/mafft-7.505/debian/mafft/usr/lib/mafft/bin
chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb
install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /build/mafft-7.505/debian/mafft/usr/lib/mafft/bin
install: WARNING: ignoring --strip-program option as -s option was not specified
chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails
strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # may fail for dash_client on mac.
install --strip-program=true dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version /build/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft
install: WARNING: ignoring --strip-program option as -s option was not specified
install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /build/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft
install: WARNING: ignoring --strip-program option as -s option was not specified
install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft
install: WARNING: ignoring --strip-program option as -s option was not specified
( cd /build/mafft-7.505/debian/mafft/usr/lib/mafft/bin; \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
ln -s mafft einsi; \
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . )
mkdir -p /build/mafft-7.505/debian/mafft/usr/share/man/man1
chmod 755 /build/mafft-7.505/debian/mafft/usr/share/man/man1
install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-7.505/debian/mafft/usr/share/man/man1
install: WARNING: ignoring --strip-program option as -s option was not specified
make[2]: Leaving directory '/build/mafft-7.505/core'
rm debian/mafft/usr/lib/mafft/lib/mafft/*.1
make[1]: Leaving directory '/build/mafft-7.505'
dh_installdocs -O--sourcedirectory=core
dh_installchangelogs -O--sourcedirectory=core
dh_installman -O--sourcedirectory=core
dh_installsystemduser -O--sourcedirectory=core
dh_perl -O--sourcedirectory=core
dh_link -O--sourcedirectory=core
dh_strip_nondeterminism -O--sourcedirectory=core
debian/rules override_dh_compress
make[1]: Entering directory '/build/mafft-7.505'
dh_compress -X test/sample
make[1]: Leaving directory '/build/mafft-7.505'
dh_fixperms -O--sourcedirectory=core
dh_missing -O--sourcedirectory=core
dh_dwz -a -O--sourcedirectory=core
dwz: debian/mafft/usr/lib/mafft/lib/mafft/addsingle: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/contrafoldwrap: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/countlen: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/disttbfast: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndblast: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndfast7: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndpre: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/dvtditr: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/f2cl: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/filter: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/getlag: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/hex2maffttext: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/maffttext2hex: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/makedirectionlist: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/mccaskillwrap: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/multi2hat3s: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/nodepair: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairash: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairlocalalign: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/regtable2seq: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/replaceu: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/restoreu: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/score: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/seq2regtable: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/setcore: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/setdirection: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/sextet5: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/splittbfast: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/tbfast: .debug_info section not present
dwz: debian/mafft/usr/lib/mafft/lib/mafft/version: .debug_info section not present
dwz: Too few files for multifile optimization
dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it.
dh_dwz: warning: Common issues include no debug information at all (missing -g) and
dh_dwz: warning: compressed debug information (#931891).
dh_strip -a -O--sourcedirectory=core
dh_makeshlibs -a -O--sourcedirectory=core
dh_shlibdeps -a -O--sourcedirectory=core
dh_installdeb -O--sourcedirectory=core
dh_gencontrol -O--sourcedirectory=core
dh_md5sums -O--sourcedirectory=core
dh_builddeb -O--sourcedirectory=core
dpkg-deb: building package 'mafft' in '../mafft_7.505-1_i386.deb'.
dpkg-genbuildinfo --build=binary -O../mafft_7.505-1_i386.buildinfo
dpkg-genchanges --build=binary -O../mafft_7.505-1_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)
dpkg-genchanges: info: including full source code in upload
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/28466 and its subdirectories
I: Current time: Wed Apr 12 23:23:40 -12 2023
I: pbuilder-time-stamp: 1681385020