Diff of the two buildlogs:

--
--- b1/build.log	2021-07-03 09:41:06.347334569 +0000
+++ b2/build.log	2021-07-03 09:42:47.743539449 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Fri Aug  5 04:02:18 -12 2022
-I: pbuilder-time-stamp: 1659715338
+I: Current time: Sat Jul  3 23:41:08 +14 2021
+I: pbuilder-time-stamp: 1625305268
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
 I: copying local configuration
@@ -17,7 +17,7 @@
 I: Extracting source
 gpgv: unknown type of key resource 'trustedkeys.kbx'
 gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
-gpgv: Signature made Wed Jul 18 07:15:32 2018 -12
+gpgv: Signature made Thu Jul 19 09:15:32 2018 +14
 gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 gpgv:                issuer "tille@debian.org"
 gpgv: Can't check signature: No public key
@@ -27,136 +27,170 @@
 dpkg-source: info: unpacking clustalo_1.2.4-2.debian.tar.xz
 I: using fakeroot in build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/11527/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/27259/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos1-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
+Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
+Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
+Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/27259/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/27259/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='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
-  DISTRIBUTION=''
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.0.3(1)-release'
+  BUILDDIR=/build
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
+  DIRSTACK=()
+  DISTRIBUTION=
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='d1a7754c9d684a68a7fed1834fd9c705'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  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='11527'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=bd92a3af3e214db8a604f4a2db18e6f3
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=27259
   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.uXpNbqHtOe/pbuilderrc_L1HH --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uXpNbqHtOe/b1 --logfile b1/build.log clustalo_1.2.4-2.dsc'
-  SUDO_GID='110'
-  SUDO_UID='105'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://85.184.249.68:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.uXpNbqHtOe/pbuilderrc_99XG --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uXpNbqHtOe/b2 --logfile b2/build.log clustalo_1.2.4-2.dsc'
+  SUDO_GID=110
+  SUDO_UID=105
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://78.137.99.97:3128
 I: uname -a
-  Linux ionos5-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux
 I: ls -l /bin
   total 5116
-  -rwxr-xr-x 1 root root 1168776 Apr 17  2019 bash
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bunzip2
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bzcat
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzcmp -> bzdiff
-  -rwxr-xr-x 1 root root    2227 Jul 10  2019 bzdiff
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzegrep -> bzgrep
-  -rwxr-xr-x 1 root root    4877 Jun 24  2019 bzexe
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzfgrep -> bzgrep
-  -rwxr-xr-x 1 root root    3641 Jul 10  2019 bzgrep
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bzip2
-  -rwxr-xr-x 1 root root   14328 Jul 10  2019 bzip2recover
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzless -> bzmore
-  -rwxr-xr-x 1 root root    1297 Jul 10  2019 bzmore
-  -rwxr-xr-x 1 root root   43744 Feb 28  2019 cat
-  -rwxr-xr-x 1 root root   64320 Feb 28  2019 chgrp
-  -rwxr-xr-x 1 root root   64288 Feb 28  2019 chmod
-  -rwxr-xr-x 1 root root   72512 Feb 28  2019 chown
-  -rwxr-xr-x 1 root root  146880 Feb 28  2019 cp
-  -rwxr-xr-x 1 root root  121464 Jan 17  2019 dash
-  -rwxr-xr-x 1 root root  109408 Feb 28  2019 date
-  -rwxr-xr-x 1 root root   76712 Feb 28  2019 dd
-  -rwxr-xr-x 1 root root   93744 Feb 28  2019 df
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 dir
-  -rwxr-xr-x 1 root root   84288 Jan  9  2019 dmesg
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 dnsdomainname -> hostname
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 domainname -> hostname
-  -rwxr-xr-x 1 root root   39520 Feb 28  2019 echo
-  -rwxr-xr-x 1 root root      28 Jan  7  2019 egrep
-  -rwxr-xr-x 1 root root   35424 Feb 28  2019 false
-  -rwxr-xr-x 1 root root      28 Jan  7  2019 fgrep
-  -rwxr-xr-x 1 root root   68880 Jan  9  2019 findmnt
-  -rwsr-xr-x 1 root root   34896 Apr 22  2020 fusermount
-  -rwxr-xr-x 1 root root  198976 Jan  7  2019 grep
-  -rwxr-xr-x 2 root root    2345 Jan  5  2019 gunzip
-  -rwxr-xr-x 1 root root    6375 Jan  5  2019 gzexe
-  -rwxr-xr-x 1 root root   98048 Jan  5  2019 gzip
-  -rwxr-xr-x 1 root root   26696 Sep 26  2018 hostname
-  -rwxr-xr-x 1 root root   68552 Feb 28  2019 ln
-  -rwxr-xr-x 1 root root   56760 Jul 26  2018 login
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 ls
-  -rwxr-xr-x 1 root root  108624 Jan  9  2019 lsblk
-  -rwxr-xr-x 1 root root   89088 Feb 28  2019 mkdir
-  -rwxr-xr-x 1 root root   68544 Feb 28  2019 mknod
-  -rwxr-xr-x 1 root root   43808 Feb 28  2019 mktemp
-  -rwxr-xr-x 1 root root   43008 Jan  9  2019 more
-  -rwsr-xr-x 1 root root   51280 Jan  9  2019 mount
-  -rwxr-xr-x 1 root root   14408 Jan  9  2019 mountpoint
-  -rwxr-xr-x 1 root root  138728 Feb 28  2019 mv
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 nisdomainname -> hostname
-  lrwxrwxrwx 1 root root      14 Feb 14  2019 pidof -> /sbin/killall5
-  -rwxr-xr-x 1 root root   39616 Feb 28  2019 pwd
-  lrwxrwxrwx 1 root root       4 Apr 17  2019 rbash -> bash
-  -rwxr-xr-x 1 root root   47776 Feb 28  2019 readlink
-  -rwxr-xr-x 1 root root   68416 Feb 28  2019 rm
-  -rwxr-xr-x 1 root root   47776 Feb 28  2019 rmdir
-  -rwxr-xr-x 1 root root   23312 Jan 21  2019 run-parts
-  -rwxr-xr-x 1 root root  122224 Dec 22  2018 sed
-  lrwxrwxrwx 1 root root       4 Jul 24 02:46 sh -> dash
-  -rwxr-xr-x 1 root root   39552 Feb 28  2019 sleep
-  -rwxr-xr-x 1 root root   80672 Feb 28  2019 stty
-  -rwsr-xr-x 1 root root   63568 Jan  9  2019 su
-  -rwxr-xr-x 1 root root   35488 Feb 28  2019 sync
-  -rwxr-xr-x 1 root root  445560 Apr 23  2019 tar
-  -rwxr-xr-x 1 root root   14440 Jan 21  2019 tempfile
-  -rwxr-xr-x 1 root root   97152 Feb 28  2019 touch
-  -rwxr-xr-x 1 root root   35424 Feb 28  2019 true
-  -rwxr-xr-x 1 root root   14328 Apr 22  2020 ulockmgr_server
-  -rwsr-xr-x 1 root root   34888 Jan  9  2019 umount
-  -rwxr-xr-x 1 root root   39584 Feb 28  2019 uname
-  -rwxr-xr-x 2 root root    2345 Jan  5  2019 uncompress
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 vdir
-  -rwxr-xr-x 1 root root   34896 Jan  9  2019 wdctl
-  -rwxr-xr-x 1 root root     946 Jan 21  2019 which
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 ypdomainname -> hostname
-  -rwxr-xr-x 1 root root    1983 Jan  5  2019 zcat
-  -rwxr-xr-x 1 root root    1677 Jan  5  2019 zcmp
-  -rwxr-xr-x 1 root root    5879 Jan  5  2019 zdiff
-  -rwxr-xr-x 1 root root      29 Jan  5  2019 zegrep
-  -rwxr-xr-x 1 root root      29 Jan  5  2019 zfgrep
-  -rwxr-xr-x 1 root root    2080 Jan  5  2019 zforce
-  -rwxr-xr-x 1 root root    7584 Jan  5  2019 zgrep
-  -rwxr-xr-x 1 root root    2205 Jan  5  2019 zless
-  -rwxr-xr-x 1 root root    1841 Jan  5  2019 zmore
-  -rwxr-xr-x 1 root root    4552 Jan  5  2019 znew
-I: user script /srv/workspace/pbuilder/11527/tmp/hooks/D02_print_environment finished
+  -rwxr-xr-x 1 root root 1168776 Apr 18  2019 bash
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bunzip2
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bzcat
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzcmp -> bzdiff
+  -rwxr-xr-x 1 root root    2227 Jul 11  2019 bzdiff
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzegrep -> bzgrep
+  -rwxr-xr-x 1 root root    4877 Jun 25  2019 bzexe
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzfgrep -> bzgrep
+  -rwxr-xr-x 1 root root    3641 Jul 11  2019 bzgrep
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bzip2
+  -rwxr-xr-x 1 root root   14328 Jul 11  2019 bzip2recover
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzless -> bzmore
+  -rwxr-xr-x 1 root root    1297 Jul 11  2019 bzmore
+  -rwxr-xr-x 1 root root   43744 Mar  1  2019 cat
+  -rwxr-xr-x 1 root root   64320 Mar  1  2019 chgrp
+  -rwxr-xr-x 1 root root   64288 Mar  1  2019 chmod
+  -rwxr-xr-x 1 root root   72512 Mar  1  2019 chown
+  -rwxr-xr-x 1 root root  146880 Mar  1  2019 cp
+  -rwxr-xr-x 1 root root  121464 Jan 18  2019 dash
+  -rwxr-xr-x 1 root root  109408 Mar  1  2019 date
+  -rwxr-xr-x 1 root root   76712 Mar  1  2019 dd
+  -rwxr-xr-x 1 root root   93744 Mar  1  2019 df
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 dir
+  -rwxr-xr-x 1 root root   84288 Jan 10  2019 dmesg
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 dnsdomainname -> hostname
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 domainname -> hostname
+  -rwxr-xr-x 1 root root   39520 Mar  1  2019 echo
+  -rwxr-xr-x 1 root root      28 Jan  8  2019 egrep
+  -rwxr-xr-x 1 root root   35424 Mar  1  2019 false
+  -rwxr-xr-x 1 root root      28 Jan  8  2019 fgrep
+  -rwxr-xr-x 1 root root   68880 Jan 10  2019 findmnt
+  -rwsr-xr-x 1 root root   34896 Apr 23  2020 fusermount
+  -rwxr-xr-x 1 root root  198976 Jan  8  2019 grep
+  -rwxr-xr-x 2 root root    2345 Jan  6  2019 gunzip
+  -rwxr-xr-x 1 root root    6375 Jan  6  2019 gzexe
+  -rwxr-xr-x 1 root root   98048 Jan  6  2019 gzip
+  -rwxr-xr-x 1 root root   26696 Sep 27  2018 hostname
+  -rwxr-xr-x 1 root root   68552 Mar  1  2019 ln
+  -rwxr-xr-x 1 root root   56760 Jul 27  2018 login
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 ls
+  -rwxr-xr-x 1 root root  108624 Jan 10  2019 lsblk
+  -rwxr-xr-x 1 root root   89088 Mar  1  2019 mkdir
+  -rwxr-xr-x 1 root root   68544 Mar  1  2019 mknod
+  -rwxr-xr-x 1 root root   43808 Mar  1  2019 mktemp
+  -rwxr-xr-x 1 root root   43008 Jan 10  2019 more
+  -rwsr-xr-x 1 root root   51280 Jan 10  2019 mount
+  -rwxr-xr-x 1 root root   14408 Jan 10  2019 mountpoint
+  -rwxr-xr-x 1 root root  138728 Mar  1  2019 mv
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 nisdomainname -> hostname
+  lrwxrwxrwx 1 root root      14 Feb 15  2019 pidof -> /sbin/killall5
+  -rwxr-xr-x 1 root root   39616 Mar  1  2019 pwd
+  lrwxrwxrwx 1 root root       4 Apr 18  2019 rbash -> bash
+  -rwxr-xr-x 1 root root   47776 Mar  1  2019 readlink
+  -rwxr-xr-x 1 root root   68416 Mar  1  2019 rm
+  -rwxr-xr-x 1 root root   47776 Mar  1  2019 rmdir
+  -rwxr-xr-x 1 root root   23312 Jan 22  2019 run-parts
+  -rwxr-xr-x 1 root root  122224 Dec 23  2018 sed
+  lrwxrwxrwx 1 root root       4 Jul  3 23:41 sh -> bash
+  lrwxrwxrwx 1 root root       4 Jun 21 22:24 sh.distrib -> dash
+  -rwxr-xr-x 1 root root   39552 Mar  1  2019 sleep
+  -rwxr-xr-x 1 root root   80672 Mar  1  2019 stty
+  -rwsr-xr-x 1 root root   63568 Jan 10  2019 su
+  -rwxr-xr-x 1 root root   35488 Mar  1  2019 sync
+  -rwxr-xr-x 1 root root  445560 Apr 24  2019 tar
+  -rwxr-xr-x 1 root root   14440 Jan 22  2019 tempfile
+  -rwxr-xr-x 1 root root   97152 Mar  1  2019 touch
+  -rwxr-xr-x 1 root root   35424 Mar  1  2019 true
+  -rwxr-xr-x 1 root root   14328 Apr 23  2020 ulockmgr_server
+  -rwsr-xr-x 1 root root   34888 Jan 10  2019 umount
+  -rwxr-xr-x 1 root root   39584 Mar  1  2019 uname
+  -rwxr-xr-x 2 root root    2345 Jan  6  2019 uncompress
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 vdir
+  -rwxr-xr-x 1 root root   34896 Jan 10  2019 wdctl
+  -rwxr-xr-x 1 root root     946 Jan 22  2019 which
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 ypdomainname -> hostname
+  -rwxr-xr-x 1 root root    1983 Jan  6  2019 zcat
+  -rwxr-xr-x 1 root root    1677 Jan  6  2019 zcmp
+  -rwxr-xr-x 1 root root    5879 Jan  6  2019 zdiff
+  -rwxr-xr-x 1 root root      29 Jan  6  2019 zegrep
+  -rwxr-xr-x 1 root root      29 Jan  6  2019 zfgrep
+  -rwxr-xr-x 1 root root    2080 Jan  6  2019 zforce
+  -rwxr-xr-x 1 root root    7584 Jan  6  2019 zgrep
+  -rwxr-xr-x 1 root root    2205 Jan  6  2019 zless
+  -rwxr-xr-x 1 root root    1841 Jan  6  2019 zmore
+  -rwxr-xr-x 1 root root    4552 Jan  6  2019 znew
+I: user script /srv/workspace/pbuilder/27259/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -298,7 +332,7 @@
 Get: 94 http://deb.debian.org/debian buster/main amd64 libjs-underscore all 1.9.1~dfsg-1+deb10u1 [100.0 kB]
 Get: 95 http://deb.debian.org/debian buster/main amd64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB]
 Get: 96 http://deb.debian.org/debian buster/main amd64 sphinx-common all 1.8.4-1 [500 kB]
-Fetched 60.3 MB in 1s (76.1 MB/s)
+Fetched 60.3 MB in 1s (71.6 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libbsd0:amd64.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19195 files and directories currently installed.)
@@ -710,7 +744,7 @@
 fakeroot is already the newest version (1.23-1).
 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 I: Building the package
-I: Running cd /build/clustalo-1.2.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
+I: Running cd /build/clustalo-1.2.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b
 dpkg-buildpackage: info: source package clustalo
 dpkg-buildpackage: info: source version 1.2.4-2
 dpkg-buildpackage: info: source distribution unstable
@@ -1040,7 +1074,7 @@
 # nothing to do here
 make[1]: Leaving directory '/build/clustalo-1.2.4'
    dh_auto_build -Nlibclustalo-doc
-	make -j16
+	make -j15
 make[1]: Entering directory '/build/clustalo-1.2.4'
 Making all in src
 make[2]: Entering directory '/build/clustalo-1.2.4/src'
@@ -1048,10 +1082,10 @@
 make[3]: Entering directory '/build/clustalo-1.2.4/src'
 Making all in hhalign
 make[4]: Entering directory '/build/clustalo-1.2.4/src/hhalign'
-/bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp
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+/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libhhalign.la  hhalign.lo  -largtable2 -lm 
 libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o 
 ar: `u' modifier ignored since `D' is the default (see `U')
 libtool: link: ranlib .libs/libhhalign.a
@@ -1059,118 +1093,118 @@
 make[4]: Leaving directory '/build/clustalo-1.2.4/src/hhalign'
 Making all in squid
 make[4]: Entering directory '/build/clustalo-1.2.4/src/squid'
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-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c dayhoff.c  -fPIC -DPIC -o .libs/dayhoff.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c  -fPIC -DPIC -o .libs/hsregex.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o a2m.lo a2m.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignio.lo alignio.c
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+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c
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+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file.lo file.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getopt.lo getopt.c
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+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi.lo gsi.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iupac.lo iupac.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o msa.lo msa.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c  -fPIC -DPIC -o .libs/clustal.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c  -fPIC -DPIC -o .libs/alignio.o
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-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c  -fPIC -DPIC -o .libs/cluster.o
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-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c  -fPIC -DPIC -o .libs/clustal.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c  -fPIC -DPIC -o .libs/alignio.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c  -fPIC -DPIC -o .libs/msa.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c  -fPIC -DPIC -o .libs/gsi.o
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+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c dayhoff.c  -fPIC -DPIC -o .libs/dayhoff.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c  -fPIC -DPIC -o .libs/file.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c  -fPIC -DPIC -o .libs/cluster.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c  -fPIC -DPIC -o .libs/hsregex.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c  -fPIC -DPIC -o .libs/msa.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c eps.c  -fPIC -DPIC -o .libs/eps.o
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-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msf.c  -fPIC -DPIC -o .libs/msf.o
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 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c iupac.c -o iupac.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o msf.lo msf.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gki.c -o gki.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c getopt.c -o getopt.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c  -fPIC -DPIC -o .libs/phylip.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c -o gsi.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rk.lo rk.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o selex.lo selex.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqencode.lo seqencode.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msf.c  -fPIC -DPIC -o .libs/msf.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip.lo phylip.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msf.c -o msf.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle.lo shuffle.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rk.lo rk.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o selex.lo selex.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqencode.lo seqencode.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c  -fPIC -DPIC -o .libs/phylip.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle.lo shuffle.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c revcomp.c  -fPIC -DPIC -o .libs/revcomp.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c -o phylip.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c rk.c  -fPIC -DPIC -o .libs/rk.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sqerror.lo sqerror.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sqerror.lo sqerror.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sqio.lo sqio.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c selex.c  -fPIC -DPIC -o .libs/selex.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sqio.lo sqio.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seqencode.c  -fPIC -DPIC -o .libs/seqencode.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c rk.c  -fPIC -DPIC -o .libs/rk.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c shuffle.c  -fPIC -DPIC -o .libs/shuffle.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqerror.c  -fPIC -DPIC -o .libs/sqerror.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seqencode.c  -fPIC -DPIC -o .libs/seqencode.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c revcomp.c -o revcomp.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c -o phylip.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqerror.c  -fPIC -DPIC -o .libs/sqerror.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msf.c -o msf.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c rk.c -o rk.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqio.c  -fPIC -DPIC -o .libs/sqio.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o squidcore.lo squidcore.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_ctype.lo sre_ctype.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqerror.c -o sqerror.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_math.lo sre_math.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c squidcore.c  -fPIC -DPIC -o .libs/squidcore.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o squidcore.lo squidcore.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_ctype.lo sre_ctype.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seqencode.c -o seqencode.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_random.lo sre_random.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c -o msa.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_math.lo sre_math.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_random.lo sre_random.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_string.lo sre_string.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_ctype.c  -fPIC -DPIC -o .libs/sre_ctype.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sre_string.lo sre_string.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ssi.lo ssi.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stack.lo stack.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ssi.lo ssi.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c squidcore.c  -fPIC -DPIC -o .libs/squidcore.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stack.lo stack.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_random.c  -fPIC -DPIC -o .libs/sre_random.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c squidcore.c -o squidcore.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stockholm.lo stockholm.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_math.c  -fPIC -DPIC -o .libs/sre_math.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stopwatch.lo stopwatch.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.lo translate.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_random.c  -fPIC -DPIC -o .libs/sre_random.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ssi.c  -fPIC -DPIC -o .libs/ssi.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_string.c  -fPIC -DPIC -o .libs/sre_string.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c -o msa.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ssi.c  -fPIC -DPIC -o .libs/ssi.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c shuffle.c -o shuffle.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stockholm.lo stockholm.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stopwatch.lo stopwatch.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_ctype.c -o sre_ctype.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stack.c  -fPIC -DPIC -o .libs/stack.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stopwatch.c  -fPIC -DPIC -o .libs/stopwatch.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.lo translate.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o types.lo types.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vectorops.lo vectorops.c
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_random.c -o sre_random.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stockholm.c  -fPIC -DPIC -o .libs/stockholm.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stopwatch.c  -fPIC -DPIC -o .libs/stopwatch.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c  -fPIC -DPIC -o .libs/translate.o
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o types.lo types.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vectorops.lo vectorops.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stack.c -o stack.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_math.c -o sre_math.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_random.c -o sre_random.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weight.lo weight.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stopwatch.c -o stopwatch.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c types.c  -fPIC -DPIC -o .libs/types.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_math.c -o sre_math.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stack.c -o stack.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c selex.c -o selex.o >/dev/null 2>&1
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weight.lo weight.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_string.c -o sre_string.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -o translate.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c vectorops.c  -fPIC -DPIC -o .libs/vectorops.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c selex.c -o selex.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -o translate.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stopwatch.c -o stopwatch.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weight.c  -fPIC -DPIC -o .libs/weight.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c types.c -o types.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqio.c -o sqio.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c vectorops.c -o vectorops.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c stockholm.c -o stockholm.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ssi.c -o ssi.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c sqio.c -o sqio.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weight.c -o weight.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=link gcc -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libsquid.la  a2m.lo aligneval.lo alignio.lo clustal.lo cluster.lo dayhoff.lo eps.lo file.lo getopt.lo gki.lo gsi.lo gsi64.lo hsregex.lo iupac.lo msa.lo msf.lo phylip.lo revcomp.lo rk.lo selex.lo seqencode.lo shuffle.lo sqerror.lo sqio.lo squidcore.lo sre_ctype.lo sre_math.lo sre_random.lo sre_string.lo ssi.lo stack.lo stockholm.lo stopwatch.lo translate.lo types.lo vectorops.lo weight.lo  -largtable2 -lm 
+/bin/sh ../../libtool  --tag=CC   --mode=link gcc -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libsquid.la  a2m.lo aligneval.lo alignio.lo clustal.lo cluster.lo dayhoff.lo eps.lo file.lo getopt.lo gki.lo gsi.lo gsi64.lo hsregex.lo iupac.lo msa.lo msf.lo phylip.lo revcomp.lo rk.lo selex.lo seqencode.lo shuffle.lo sqerror.lo sqio.lo squidcore.lo sre_ctype.lo sre_math.lo sre_random.lo sre_string.lo ssi.lo stack.lo stockholm.lo stopwatch.lo translate.lo types.lo vectorops.lo weight.lo  -largtable2 -lm 
 libtool: link: ar cru .libs/libsquid.a .libs/a2m.o .libs/aligneval.o .libs/alignio.o .libs/clustal.o .libs/cluster.o .libs/dayhoff.o .libs/eps.o .libs/file.o .libs/getopt.o .libs/gki.o .libs/gsi.o .libs/gsi64.o .libs/hsregex.o .libs/iupac.o .libs/msa.o .libs/msf.o .libs/phylip.o .libs/revcomp.o .libs/rk.o .libs/selex.o .libs/seqencode.o .libs/shuffle.o .libs/sqerror.o .libs/sqio.o .libs/squidcore.o .libs/sre_ctype.o .libs/sre_math.o .libs/sre_random.o .libs/sre_string.o .libs/ssi.o .libs/stack.o .libs/stockholm.o .libs/stopwatch.o .libs/translate.o .libs/types.o .libs/vectorops.o .libs/weight.o 
 ar: `u' modifier ignored since `D' is the default (see `U')
 libtool: link: ranlib .libs/libsquid.a
@@ -1178,16 +1212,16 @@
 make[4]: Leaving directory '/build/clustalo-1.2.4/src/squid'
 Making all in kmpp
 make[4]: Entering directory '/build/clustalo-1.2.4/src/kmpp'
-/bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KMeans.lo KMeans.cpp
-/bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KmTree.lo KmTree.cpp
-/bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KmUtils.lo KmUtils.cpp
-libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KMeans.cpp  -fPIC -DPIC -o .libs/KMeans.o
+/bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KMeans.lo KMeans.cpp
+/bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KmTree.lo KmTree.cpp
+/bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o KmUtils.lo KmUtils.cpp
 libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KmTree.cpp  -fPIC -DPIC -o .libs/KmTree.o
+libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KMeans.cpp  -fPIC -DPIC -o .libs/KMeans.o
 libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KmUtils.cpp  -fPIC -DPIC -o .libs/KmUtils.o
 libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KmUtils.cpp -o KmUtils.o >/dev/null 2>&1
 libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KmTree.cpp -o KmTree.o >/dev/null 2>&1
 libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c KMeans.cpp -o KMeans.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CXX   --mode=link g++ -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libkmpp.la  KMeans.lo KmTree.lo KmUtils.lo  -largtable2 -lm 
+/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -DCLUSTALO  -O3  -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libkmpp.la  KMeans.lo KmTree.lo KmUtils.lo  -largtable2 -lm 
 libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o 
 ar: `u' modifier ignored since `D' is the default (see `U')
 libtool: link: ranlib .libs/libkmpp.a
@@ -1195,49 +1229,49 @@
 make[4]: Leaving directory '/build/clustalo-1.2.4/src/kmpp'
 Making all in clustal
 make[4]: Entering directory '/build/clustalo-1.2.4/src/clustal'
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign_wrapper.lo hhalign_wrapper.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ktuple_pair.lo ktuple_pair.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o list.lo list.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.lo log.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_upgma.lo muscle_upgma.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_tree.lo muscle_tree.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progress.lo progress.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.lo seq.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.c
-/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c  -fPIC -DPIC -o .libs/pair_dist.o
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign_wrapper.lo hhalign_wrapper.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ktuple_pair.lo ktuple_pair.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o list.lo list.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.lo log.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_upgma.lo muscle_upgma.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_tree.lo muscle_tree.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progress.lo progress.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.lo seq.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.c
+/bin/sh ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign_wrapper.c  -fPIC -DPIC -o .libs/hhalign_wrapper.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c  -fPIC -DPIC -o .libs/symmatrix.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c  -fPIC -DPIC -o .libs/log.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c  -fPIC -DPIC -o .libs/muscle_upgma.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c  -fPIC -DPIC -o .libs/util.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c  -fPIC -DPIC -o .libs/ktuple_pair.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c  -fPIC -DPIC -o .libs/seq.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c  -fPIC -DPIC -o .libs/muscle_tree.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c  -fPIC -DPIC -o .libs/list.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c  -fPIC -DPIC -o .libs/pair_dist.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c  -fPIC -DPIC -o .libs/mbed.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c  -fPIC -DPIC -o .libs/muscle_tree.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c  -fPIC -DPIC -o .libs/progress.o
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c  -fPIC -DPIC -o .libs/tree.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c  -fPIC -DPIC -o .libs/util.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c  -fPIC -DPIC -o .libs/muscle_upgma.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c  -fPIC -DPIC -o .libs/seq.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c  -fPIC -DPIC -o .libs/symmatrix.o
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c  -fPIC -DPIC -o .libs/weights.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c  -fPIC -DPIC -o .libs/tree.o
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c -o list.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -o log.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1
-libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -o pair_dist.o >/dev/null 2>&1
+libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -o mbed.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1
-/bin/bash ../../libtool  --tag=CC   --mode=link gcc -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libclustal.la  hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo  -largtable2 -lm 
+/bin/sh ../../libtool  --tag=CC   --mode=link gcc -fopenmp  -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o libclustal.la  hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo  -largtable2 -lm 
 libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o 
 ar: `u' modifier ignored since `D' is the default (see `U')
 libtool: link: ranlib .libs/libclustal.a
@@ -1246,14 +1280,14 @@
 make[4]: Entering directory '/build/clustalo-1.2.4/src'
 g++ -DHAVE_CONFIG_H -I.   -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp
 gcc -DHAVE_CONFIG_H -I.   -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c
-/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.   -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
+/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.   -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c  -fPIC -DPIC -o .libs/clustal-omega.o
 clustal-omega.c: In function 'PrintLongVersion':
 clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
               PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
                                                  ^~~~~~~~
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1
-/bin/bash ../libtool  --tag=CC   --mode=link gcc -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/x86_64-linux-gnu clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la  -largtable2 -lm 
+/bin/sh ../libtool  --tag=CC   --mode=link gcc -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/x86_64-linux-gnu clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la  -largtable2 -lm 
 libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/build/clustalo-1.2.4/src/clustal/.libs/libclustal.a")
 libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/build/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a")
 libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/build/clustalo-1.2.4/src/squid/.libs/libsquid.a")
@@ -1263,7 +1297,7 @@
 libtool: link: ranlib .libs/libclustalo.a
 libtool: link: rm -fr .libs/libclustalo.lax
 libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
-/bin/bash ../libtool  --tag=CXX   --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm 
+/bin/sh ../libtool  --tag=CXX   --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm 
 libtool: link: g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o  ./.libs/libclustalo.a /usr/lib/x86_64-linux-gnu/libargtable2.so -lm -fopenmp
 /usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile':
 ./src/clustal-omega.c:393: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
@@ -1279,7 +1313,7 @@
 # nothing to do here
 make[1]: Leaving directory '/build/clustalo-1.2.4'
    dh_auto_test -Nlibclustalo-doc
-	make -j16 check VERBOSE=1
+	make -j15 check VERBOSE=1
 make[1]: Entering directory '/build/clustalo-1.2.4'
 Making check in src
 make[2]: Entering directory '/build/clustalo-1.2.4/src'
@@ -1353,14 +1387,14 @@
 make[4]: Entering directory '/build/clustalo-1.2.4/src'
 make[5]: Entering directory '/build/clustalo-1.2.4/src'
  /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu'
- /bin/bash ../libtool   --mode=install /usr/bin/install -c   libclustalo.la '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu'
+ /bin/sh ../libtool   --mode=install /usr/bin/install -c   libclustalo.la '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu'
 libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.la
 libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a
 libtool: install: chmod 644 /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a
 libtool: install: ranlib /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a
 libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
  /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/bin'
-  /bin/bash ../libtool   --mode=install /usr/bin/install -c clustalo '/build/clustalo-1.2.4/debian/tmp/usr/bin'
+  /bin/sh ../libtool   --mode=install /usr/bin/install -c clustalo '/build/clustalo-1.2.4/debian/tmp/usr/bin'
 libtool: install: /usr/bin/install -c clustalo /build/clustalo-1.2.4/debian/tmp/usr/bin/clustalo
  /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/'
  /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/'
@@ -1468,26 +1502,28 @@
    dh_shlibdeps
    dh_installdeb
    dh_gencontrol
-dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined
 dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined
+dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined
    dh_md5sums
    dh_builddeb
 dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-2_all.deb'.
+dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-2_amd64.deb'.
 dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-2_amd64.deb'.
 dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-2_amd64.deb'.
-dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-2_amd64.deb'.
  dpkg-genbuildinfo --build=binary
  dpkg-genchanges --build=binary >../clustalo_1.2.4-2_amd64.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: user script /srv/workspace/pbuilder/27259/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/27259/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/11527 and its subdirectories
-I: Current time: Fri Aug  5 04:04:05 -12 2022
-I: pbuilder-time-stamp: 1659715445
+I: removing directory /srv/workspace/pbuilder/27259 and its subdirectories
+I: Current time: Sat Jul  3 23:42:47 +14 2021
+I: pbuilder-time-stamp: 1625305367