W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 19 18:53:32 +14 2023 I: pbuilder-time-stamp: 1681880012 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 [staden_2.0.0+b11-4.dsc] I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 13 02:48:12 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./staden_2.0.0+b11-4.dsc: no acceptable signature found dpkg-source: info: extracting staden in staden-2.0.0+b11 dpkg-source: info: unpacking staden_2.0.0+b11.orig.tar.gz dpkg-source: info: unpacking staden_2.0.0+b11-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying make_help_menus_work.patch dpkg-source: info: applying fix_tcl_path.patch dpkg-source: info: applying fix_awk.patch dpkg-source: info: applying enable_setting_stadenroot.patch dpkg-source: info: applying include_xalloc.patch dpkg-source: info: applying use_mkstemp_instead_of_tmpnam.patch dpkg-source: info: applying fix_implicit_declaration.patch dpkg-source: info: applying autoconfig.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19802/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 19 18:53 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/19802/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/19802/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=19802 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MUSEEKMu/pbuilderrc_U2Pf --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MUSEEKMu/b2 --logfile b2/build.log --extrapackages usrmerge staden_2.0.0+b11-4.dsc' SUDO_GID=112 SUDO_UID=107 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 i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 10:21 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:21 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 19 18:53 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/19802/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 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 (>= 12~), libstaden-read-dev (>= 1.14.6), itcl3-dev, itk3-dev, zlib1g-dev, libbz2-dev, liblzma-dev, tcl-dev, tk-dev, tklib, libpng-dev, libncurses5-dev, iwidgets4, libcurl4-gnutls-dev 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 (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev (>= 1.14.6); however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on itcl3-dev; however: Package itcl3-dev is not installed. pbuilder-satisfydepends-dummy depends on itk3-dev; however: Package itk3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on tcl-dev; however: Package tcl-dev is not installed. pbuilder-satisfydepends-dummy depends on tk-dev; however: Package tk-dev is not installed. pbuilder-satisfydepends-dummy depends on tklib; however: Package tklib is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on iwidgets4; however: Package iwidgets4 is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev 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} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} itcl3{a} itcl3-dev{a} itk3{a} itk3-dev{a} iwidgets4{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpng-dev{a} libpng16-16{a} libpsl5{a} libpthread-stubs0-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libstaden-read-dev{a} libstaden-read14{a} libsub-override-perl{a} libtcl8.6{a} libtk8.6{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft-dev{a} libxft2{a} libxml2{a} libxrender-dev{a} libxrender1{a} libxss-dev{a} libxss1{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tcl{a} tcl-dev{a} tcl8.6{a} tcl8.6-dev{a} tk{a} tk-dev{a} tk8.6{a} tk8.6-dev{a} tklib{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules lynx publicsuffix tcllib wget 0 packages upgraded, 107 newly installed, 0 to remove and 0 not upgraded. Need to get 40.7 MB of archives. After unpacking 137 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-4 [410 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 itcl3 i386 3.4.4-2 [54.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 itk3 i386 3.4.2-3.1 [31.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 43 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 tcl8.6 i386 8.6.13+dfsg-2 [120 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 tcl8.6-dev i386 8.6.13+dfsg-2 [1111 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 tcl i386 8.6.13 [4016 B] Get: 57 http://deb.debian.org/debian bookworm/main i386 tcl-dev i386 8.6.13 [6552 B] Get: 58 http://deb.debian.org/debian bookworm/main i386 itcl3-dev i386 3.4.4-2 [15.6 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 x11proto-dev all 2022.1-1 [599 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 x11proto-core-dev all 2022.1-1 [3528 B] Get: 62 http://deb.debian.org/debian bookworm/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 66 http://deb.debian.org/debian bookworm/main i386 libxcb1-dev i386 1.15-1 [185 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libx11-dev i386 2:1.8.4-2 [866 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libxext-dev i386 2:1.3.4-1+b1 [110 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libxss-dev i386 1:1.2.3-1 [23.8 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libbrotli-dev i386 1.0.9-2+b6 [287 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libpng-dev i386 1.6.39-2 [367 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libfreetype-dev i386 2.12.1+dfsg-4 [585 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 uuid-dev i386 2.38.1-5+b1 [40.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libfontconfig-dev i386 2.14.1-4 [425 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 libfontconfig1-dev i386 2.14.1-4 [268 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libxrender-dev i386 1:0.9.10-1.1 [42.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libxft-dev i386 2.3.6-1 [82.3 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 tk8.6 i386 8.6.13-2 [69.5 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 tk8.6-dev i386 8.6.13-2 [860 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 tk i386 8.6.13 [4052 B] Get: 86 http://deb.debian.org/debian bookworm/main i386 tk-dev i386 8.6.13 [3876 B] Get: 87 http://deb.debian.org/debian bookworm/main i386 itk3-dev i386 3.4.2-3.1 [5580 B] Get: 88 http://deb.debian.org/debian bookworm/main i386 iwidgets4 all 4.1.1-2.1 [195 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libbz2-dev i386 1.0.8-5+b1 [31.5 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-8 [412 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-8 [527 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libhtscodecs-dev i386 1.3.0-4 [2846 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-2 [111 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libncurses-dev i386 6.4-2 [379 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libncurses5-dev i386 6.4-2 [932 B] Get: 105 http://deb.debian.org/debian bookworm/main i386 libstaden-read14 i386 1.14.15-1 [287 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libstaden-read-dev i386 1.14.15-1 [370 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 tklib all 0.8~20230222-1 [1406 kB] Fetched 40.7 MB in 1s (43.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libtcl8.6:i386. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../000-libtcl8.6_8.6.13+dfsg-2_i386.deb ... Unpacking libtcl8.6:i386 (8.6.13+dfsg-2) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../001-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../002-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../003-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../004-libfreetype6_2.12.1+dfsg-4_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../005-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../006-fontconfig-config_2.14.1-4_i386.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../007-libfontconfig1_2.14.1-4_i386.deb ... Unpacking libfontconfig1:i386 (2.14.1-4) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../008-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../009-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../010-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../011-libxcb1_1.15-1_i386.deb ... Unpacking libxcb1:i386 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../012-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../013-libx11-6_2%3a1.8.4-2_i386.deb ... Unpacking libx11-6:i386 (2:1.8.4-2) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:i386. Preparing to unpack .../015-libxft2_2.3.6-1_i386.deb ... Unpacking libxft2:i386 (2.3.6-1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../016-libxext6_2%3a1.3.4-1+b1_i386.deb ... Unpacking libxext6:i386 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../017-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:i386. Preparing to unpack .../018-libxss1_1%3a1.2.3-1_i386.deb ... Unpacking libxss1:i386 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:i386. Preparing to unpack .../019-libtk8.6_8.6.13-2_i386.deb ... Unpacking libtk8.6:i386 (8.6.13-2) ... Selecting previously unselected package itcl3:i386. Preparing to unpack .../020-itcl3_3.4.4-2_i386.deb ... Unpacking itcl3:i386 (3.4.4-2) ... Selecting previously unselected package itk3:i386. Preparing to unpack .../021-itk3_3.4.2-3.1_i386.deb ... Unpacking itk3:i386 (3.4.2-3.1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../022-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../023-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../024-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../025-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../026-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../027-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../028-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../029-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../030-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../031-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../032-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../033-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../034-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../035-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 .../036-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../037-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../038-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../039-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../040-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 .../041-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 .../042-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 .../043-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 .../044-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../045-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../046-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../047-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 .../048-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../049-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 .../050-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../051-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../052-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../053-tcl8.6_8.6.13+dfsg-2_i386.deb ... Unpacking tcl8.6 (8.6.13+dfsg-2) ... Selecting previously unselected package tcl8.6-dev:i386. Preparing to unpack .../054-tcl8.6-dev_8.6.13+dfsg-2_i386.deb ... Unpacking tcl8.6-dev:i386 (8.6.13+dfsg-2) ... Selecting previously unselected package tcl. Preparing to unpack .../055-tcl_8.6.13_i386.deb ... Unpacking tcl (8.6.13) ... Selecting previously unselected package tcl-dev:i386. Preparing to unpack .../056-tcl-dev_8.6.13_i386.deb ... Unpacking tcl-dev:i386 (8.6.13) ... Selecting previously unselected package itcl3-dev:i386. Preparing to unpack .../057-itcl3-dev_3.4.4-2_i386.deb ... Unpacking itcl3-dev:i386 (3.4.4-2) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../058-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../059-x11proto-dev_2022.1-1_all.deb ... Unpacking x11proto-dev (2022.1-1) ... Selecting previously unselected package x11proto-core-dev. Preparing to unpack .../060-x11proto-core-dev_2022.1-1_all.deb ... Unpacking x11proto-core-dev (2022.1-1) ... Selecting previously unselected package libxau-dev:i386. Preparing to unpack .../061-libxau-dev_1%3a1.0.9-1_i386.deb ... Unpacking libxau-dev:i386 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:i386. Preparing to unpack .../062-libxdmcp-dev_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp-dev:i386 (1:1.1.2-3) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../063-xtrans-dev_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... Selecting previously unselected package libpthread-stubs0-dev:i386. Preparing to unpack .../064-libpthread-stubs0-dev_0.4-1_i386.deb ... Unpacking libpthread-stubs0-dev:i386 (0.4-1) ... Selecting previously unselected package libxcb1-dev:i386. Preparing to unpack .../065-libxcb1-dev_1.15-1_i386.deb ... Unpacking libxcb1-dev:i386 (1.15-1) ... Selecting previously unselected package libx11-dev:i386. Preparing to unpack .../066-libx11-dev_2%3a1.8.4-2_i386.deb ... Unpacking libx11-dev:i386 (2:1.8.4-2) ... Selecting previously unselected package libxext-dev:i386. Preparing to unpack .../067-libxext-dev_2%3a1.3.4-1+b1_i386.deb ... Unpacking libxext-dev:i386 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss-dev:i386. Preparing to unpack .../068-libxss-dev_1%3a1.2.3-1_i386.deb ... Unpacking libxss-dev:i386 (1:1.2.3-1) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../069-libexpat1-dev_2.5.0-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.5.0-1) ... Selecting previously unselected package libbrotli-dev:i386. Preparing to unpack .../070-libbrotli-dev_1.0.9-2+b6_i386.deb ... Unpacking libbrotli-dev:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng-dev:i386. Preparing to unpack .../071-libpng-dev_1.6.39-2_i386.deb ... Unpacking libpng-dev:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype-dev:i386. Preparing to unpack .../072-libfreetype-dev_2.12.1+dfsg-4_i386.deb ... Unpacking libfreetype-dev:i386 (2.12.1+dfsg-4) ... Selecting previously unselected package uuid-dev:i386. Preparing to unpack .../073-uuid-dev_2.38.1-5+b1_i386.deb ... Unpacking uuid-dev:i386 (2.38.1-5+b1) ... Selecting previously unselected package libpkgconf3:i386. Preparing to unpack .../074-libpkgconf3_1.8.1-1_i386.deb ... Unpacking libpkgconf3:i386 (1.8.1-1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../075-pkgconf-bin_1.8.1-1_i386.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:i386. Preparing to unpack .../076-pkgconf_1.8.1-1_i386.deb ... Unpacking pkgconf:i386 (1.8.1-1) ... Selecting previously unselected package pkg-config:i386. Preparing to unpack .../077-pkg-config_1.8.1-1_i386.deb ... Unpacking pkg-config:i386 (1.8.1-1) ... Selecting previously unselected package libfontconfig-dev:i386. Preparing to unpack .../078-libfontconfig-dev_2.14.1-4_i386.deb ... Unpacking libfontconfig-dev:i386 (2.14.1-4) ... Selecting previously unselected package libfontconfig1-dev:i386. Preparing to unpack .../079-libfontconfig1-dev_2.14.1-4_i386.deb ... Unpacking libfontconfig1-dev:i386 (2.14.1-4) ... Selecting previously unselected package libxrender-dev:i386. Preparing to unpack .../080-libxrender-dev_1%3a0.9.10-1.1_i386.deb ... Unpacking libxrender-dev:i386 (1:0.9.10-1.1) ... Selecting previously unselected package libxft-dev:i386. Preparing to unpack .../081-libxft-dev_2.3.6-1_i386.deb ... Unpacking libxft-dev:i386 (2.3.6-1) ... Selecting previously unselected package tk8.6. Preparing to unpack .../082-tk8.6_8.6.13-2_i386.deb ... Unpacking tk8.6 (8.6.13-2) ... Selecting previously unselected package tk8.6-dev:i386. Preparing to unpack .../083-tk8.6-dev_8.6.13-2_i386.deb ... Unpacking tk8.6-dev:i386 (8.6.13-2) ... Selecting previously unselected package tk. Preparing to unpack .../084-tk_8.6.13_i386.deb ... Unpacking tk (8.6.13) ... Selecting previously unselected package tk-dev:i386. Preparing to unpack .../085-tk-dev_8.6.13_i386.deb ... Unpacking tk-dev:i386 (8.6.13) ... Selecting previously unselected package itk3-dev:i386. Preparing to unpack .../086-itk3-dev_3.4.2-3.1_i386.deb ... Unpacking itk3-dev:i386 (3.4.2-3.1) ... Selecting previously unselected package iwidgets4. Preparing to unpack .../087-iwidgets4_4.1.1-2.1_all.deb ... Unpacking iwidgets4 (4.1.1-2.1) ... Selecting previously unselected package libbz2-dev:i386. Preparing to unpack .../088-libbz2-dev_1.0.8-5+b1_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-5+b1) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../089-libsasl2-modules-db_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../090-libsasl2-2_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../091-libldap-2.5-0_2.5.13+dfsg-5_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../092-libnghttp2-14_1.52.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.52.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../093-libpsl5_0.21.2-1_i386.deb ... Unpacking libpsl5:i386 (0.21.2-1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../094-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../095-libssh2-1_1.10.0-3+b1_i386.deb ... Unpacking libssh2-1:i386 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../096-libcurl3-gnutls_7.88.1-8_i386.deb ... Unpacking libcurl3-gnutls:i386 (7.88.1-8) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../097-libcurl4-gnutls-dev_7.88.1-8_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (7.88.1-8) ... Selecting previously unselected package libhtscodecs2:i386. Preparing to unpack .../098-libhtscodecs2_1.3.0-4_i386.deb ... Unpacking libhtscodecs2:i386 (1.3.0-4) ... Selecting previously unselected package libhtscodecs-dev:i386. Preparing to unpack .../099-libhtscodecs-dev_1.3.0-4_i386.deb ... Unpacking libhtscodecs-dev:i386 (1.3.0-4) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../100-liblzma-dev_5.4.1-0.2_i386.deb ... Unpacking liblzma-dev:i386 (5.4.1-0.2) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../101-libncurses6_6.4-2_i386.deb ... Unpacking libncurses6:i386 (6.4-2) ... Selecting previously unselected package libncurses-dev:i386. Preparing to unpack .../102-libncurses-dev_6.4-2_i386.deb ... Unpacking libncurses-dev:i386 (6.4-2) ... Selecting previously unselected package libncurses5-dev:i386. Preparing to unpack .../103-libncurses5-dev_6.4-2_i386.deb ... Unpacking libncurses5-dev:i386 (6.4-2) ... Selecting previously unselected package libstaden-read14:i386. Preparing to unpack .../104-libstaden-read14_1.14.15-1_i386.deb ... Unpacking libstaden-read14:i386 (1.14.15-1) ... Selecting previously unselected package libstaden-read-dev. Preparing to unpack .../105-libstaden-read-dev_1.14.15-1_i386.deb ... Unpacking libstaden-read-dev (1.14.15-1) ... Selecting previously unselected package tklib. Preparing to unpack .../106-tklib_0.8~20230222-1_all.deb ... Unpacking tklib (0.8~20230222-1) ... Setting up libhtscodecs2:i386 (1.3.0-4) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libpsl5:i386 (0.21.2-1) ... 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 libbrotli1:i386 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:i386 (1.52.0-1) ... 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 libpthread-stubs0-dev:i386 (0.4-1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up libhtscodecs-dev:i386 (1.3.0-4) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libexpat1-dev:i386 (2.5.0-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up uuid-dev:i386 (2.38.1-5+b1) ... Setting up libncurses6:i386 (6.4-2) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up libtcl8.6:i386 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:i386 (5.4.1-0.2) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... 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 libssh2-1:i386 (1.10.0-3+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Setting up libbrotli-dev:i386 (1.0.9-2+b6) ... Setting up libbz2-dev:i386 (1.0.8-5+b1) ... 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 x11proto-dev (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up tcl8.6 (8.6.13+dfsg-2) ... Setting up libncurses-dev:i386 (6.4-2) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxau-dev:i386 (1:1.0.9-1) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up tcl8.6-dev:i386 (8.6.13+dfsg-2) ... Setting up libpng-dev:i386 (1.6.39-2) ... Setting up itcl3:i386 (3.4.4-2) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:i386 (1:1.1.2-3) ... Setting up libfreetype6:i386 (2.12.1+dfsg-4) ... Setting up x11proto-core-dev (2022.1-1) ... Setting up pkg-config:i386 (1.8.1-1) ... 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 tcl (8.6.13) ... Setting up libncurses5-dev:i386 (6.4-2) ... Setting up libx11-6:i386 (2:1.8.4-2) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up itcl3-dev:i386 (3.4.4-2) ... Setting up libxcb1-dev:i386 (1.15-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libx11-dev:i386 (2:1.8.4-2) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:i386 (7.88.1-8) ... Setting up libcurl4-gnutls-dev:i386 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libfreetype-dev:i386 (2.12.1+dfsg-4) ... Setting up tcl-dev:i386 (8.6.13) ... Setting up libxext-dev:i386 (2:1.3.4-1+b1) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libstaden-read14:i386 (1.14.15-1) ... Setting up libxrender-dev:i386 (1:0.9.10-1.1) ... Setting up libxft2:i386 (2.3.6-1) ... Setting up libfontconfig-dev:i386 (2.14.1-4) ... Setting up libtk8.6:i386 (8.6.13-2) ... Setting up libstaden-read-dev (1.14.15-1) ... Setting up debhelper (13.11.4) ... Setting up libxss-dev:i386 (1:1.2.3-1) ... Setting up itk3:i386 (3.4.2-3.1) ... Setting up iwidgets4 (4.1.1-2.1) ... Setting up libxft-dev:i386 (2.3.6-1) ... Setting up tk8.6 (8.6.13-2) ... Setting up libfontconfig1-dev:i386 (2.14.1-4) ... Setting up tk8.6-dev:i386 (8.6.13-2) ... Setting up tk (8.6.13) ... Setting up itk3-dev:i386 (3.4.2-3.1) ... Setting up tk-dev:i386 (8.6.13) ... Setting up tklib (0.8~20230222-1) ... Processing triggers for libc-bin (2.36-9) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/19802/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/19802/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/staden-2.0.0+b11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../staden_2.0.0+b11-4_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/staden-2.0.0+b11' make spotless || true make[2]: Entering directory '/build/staden-2.0.0+b11' make[2]: *** No rule to make target 'spotless'. Stop. make[2]: Leaving directory '/build/staden-2.0.0+b11' rm -f config.log config.status rm -f Makefile shlib.conf staden_config.h system.mk find -name debian -prune -o -name .dir -exec rm '{}' ';' make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:32: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:32: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/libcurl_check_config.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.in:32: the top level configure.in:33: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:33: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_zlib.m4:32: AX_LIB_ZLIB is expanded from... configure.in:33: the top level configure.in:34: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:34: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_lzma.m4:32: AX_LIB_LZMA is expanded from... configure.in:34: the top level configure.in:35: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:35: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_png.m4:34: AX_LIB_PNG is expanded from... configure.in:35: the top level configure.in:40: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:40: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_staden_io_lib.m4:35: AX_LIB_IO_LIB is expanded from... configure.in:40: the top level configure.in:43: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:43: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_curses.m4:37: AX_LIB_CURSES is expanded from... configure.in:43: the top level configure.in:46: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:46: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:46: the top level configure.in:93: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:43: TEA_PATH_TCLCONFIG is expanded from... configure.in:93: the top level configure.in:94: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:94: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:355: TEA_LOAD_TCLCONFIG is expanded from... configure.in:94: the top level configure.in:96: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:96: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:200: TEA_PATH_TKCONFIG is expanded from... configure.in:96: the top level configure.in:102: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_RUN' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:2704: TEA_TCL_EARLY_FLAG is expanded from... ac_stubs/tcl.m4:2717: TEA_TCL_EARLY_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:148: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:148: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_tklib.m4:27: AX_LIB_TKLIB is expanded from... configure.in:148: the top level configure.in:149: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:149: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_iwidgets.m4:28: AX_LIB_IWIDGETS is expanded from... configure.in:149: the top level configure.in:150: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:150: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itcl.m4:26: AX_LIB_ITCL is expanded from... configure.in:150: the top level configure.in:151: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:151: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itk.m4:26: AX_LIB_ITK is expanded from... configure.in:151: the top level autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/staden-2.0.0+b11' dh_auto_configure -- \ --with-itcl=/usr/lib/tcltk/i386-linux-gnu \ --with-itk=/usr/lib/tcltk/i386-linux-gnu ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-itcl=/usr/lib/tcltk/i386-linux-gnu --with-itk=/usr/lib/tcltk/i386-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.88.1 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking for png.h... yes checking for staden-io_lib-config... no checking for io_lib-config... /usr/bin/io_lib-config checking if io_lib version >= 1.12.5... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking for ncurses.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes checking for pwd.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGEFILE_SOURCE value needed for large files... no checking for library containing cos... -lm checking for popen... yes checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... no checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking if 64bit support is requested... no checking if 64bit Sparc VIS support is requested... no checking if compiler supports visibility "hidden"... yes checking if rpath support is requested... yes checking system version... Linux-5.10.0-21-686-pae checking for ar... ar checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... long long checking for struct dirent64... no checking for struct stat64... no checking for open64... yes checking for lseek64... yes checking for off64_t... no checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include/tcl8.6 checking for Tcl private include files... Using srcdir found in tclConfig.sh: /usr/include/tcl8.6/tcl-private checking for Tk public headers... /usr/include/tcl8.6 checking for Tk private include files... Using srcdir found in tkConfig.sh: /usr/include/tcl8.6/tk-private checking tklib directory... yes (/usr/share/tcltk/tklib0.8) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/i386-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/i386-linux-gnu/itk3.4) configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/share/tcltk/tklib0.8 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/i386-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/i386-linux-gnu/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_auto_build make -j7 make[1]: Entering directory '/build/staden-2.0.0+b11' cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc all cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev all cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src all cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all make[2]: Entering directory '/build/staden-2.0.0+b11/Misc' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts all make[2]: Entering directory '/build/staden-2.0.0+b11/trev' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/primer3' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/scripts' make[2]: warning: -j7 forced in submake: resetting jobserver mode. /build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/trev' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o crash.o -c crash.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o date.o -c date.c make[2]: Nothing to be done for 'all'. Nothing to build for Pregap4. make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data all gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c Nothing to build for scripts. make[2]: Leaving directory '/build/staden-2.0.0+b11/scripts' make[2]: Leaving directory '/build/staden-2.0.0+b11/pregap4' make[2]: Entering directory '/build/staden-2.0.0+b11/data' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shell.o -c shell.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c /build/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o -c dpal.c Nothing to build for data. make[2]: Leaving directory '/build/staden-2.0.0+b11/data' Nothing to build for spin_emboss. make[2]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o boulder_input.o -c boulder_input.c mkdir -p /build/staden-2.0.0+b11/lib 2>/dev/null touch /build/staden-2.0.0+b11/lib/.dir gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o error.o -c error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c primer3_main.c: In function 'boulder_print_oligos': primer3_main.c:416:32: warning: '%d' directive writing between 1 and 8 bytes into a region of size 2 [-Wformat-overflow=] 416 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:416:30: note: directive argument in the range [1, 56512729] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:906, from primer3_main.c:7: In function 'sprintf', inlined from 'boulder_print_oligos' at primer3_main.c:416:7: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 10 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array.o -c array.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o locks.o -c locks.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c primer3_main.c: In function 'main': primer3_main.c:234:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); | ^~ In function 'boulder_print_pairs', inlined from 'main' at primer3_main.c:109:3: primer3_main.c:234:30: note: directive argument in the range [1, 2147483646] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In function 'sprintf', inlined from 'boulder_print_pairs' at primer3_main.c:234:7, inlined from 'main' at primer3_main.c:109:3: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c parse_db.c: In function 'parse_entry': parse_db.c:234:66: warning: '%s' directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); | ^~ ~~~~ In file included from /usr/include/stdio.h:906, from parse_db.c:19: In function 'sprintf', inlined from 'parse_entry' at parse_db.c:234:7: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 33 and 8224 bytes into a destination of size 8192 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/Misc' cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi all cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf all cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g all make[2]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/text_utils' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/abi' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/alf' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/g' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba all make[2]: Entering directory '/build/staden-2.0.0+b11/eba' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./alf -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cli_arg.o -c cli_arg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXkeylist.o -c tclXkeylist.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXutil.o -c tclXutil.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_debug.o -c tcl_debug.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o misc.o -c misc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c alfsplit.c: In function 'main': alfsplit.c:347:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 363 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function 'readIndexEntry': alfsplit.c:129:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | fread (ent->label,40,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:135:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 135 | fread (junk,70,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output.o -c text_output.c make[2]: Leaving directory '/build/staden-2.0.0+b11/text_utils' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRaster.o -c tkRaster.c cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all make[2]: Entering directory '/build/staden-2.0.0+b11/init_exp' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sheet.o -c sheet.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./init_exp -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIcomment abiIO.o getABIcomment.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet.o -c tkSheet.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet_common.o -c tkSheet_common.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o alfsplit alfsplit.o -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/alf' gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all make[2]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./get_scf_field -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace_print.o -c trace_print.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o postscript.o -c postscript.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o split.o -c split.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o get_scf_field get_scf_field.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/init_exp' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTrace.o -c tkTrace.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceComp.o -c tkTraceComp.c cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins all make[2]: Entering directory '/build/staden-2.0.0+b11/hetins' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./hetins -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c make[2]: Leaving directory '/build/staden-2.0.0+b11/eba' make[2]: Leaving directory '/build/staden-2.0.0+b11/abi' make[2]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceIO.o -c tkTraceIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceDisp.o -c tkTraceDisp.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o capture.o -c capture.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o canvas_box.o -c canvas_box.c make[2]: Leaving directory '/build/staden-2.0.0+b11/g' capture.c: In function 'tcl_capture': capture.c:33:14: warning: implicit declaration of function 'mkostemp'; did you mean 'mkstemp'? [-Wimplicit-function-declaration] 33 | fd = mkostemp(NULL, 0666); | ^~~~~~~~ | mkstemp capture.c:54:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | read(fd, buf, statbuf.st_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_tick.o -c ruler_tick.c tkTraceDisp.c: In function 'trace_draw_numbers': tkTraceDisp.c:746:32: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 746 | sprintf(number, "%d", cind); | ^ In file included from /usr/include/stdio.h:906, from tkTraceDisp.c:2: In function 'sprintf', inlined from 'trace_draw_numbers' at tkTraceDisp.c:746:6: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzyme_map.o -c restriction_enzyme_map.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o hetins hetins.o -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o element_canvas.o -c element_canvas.c make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container.o -c container.c make[2]: Leaving directory '/build/staden-2.0.0+b11/hetins' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container_ruler.o -c container_ruler.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_io_lib.o -c tcl_io_lib.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all make[2]: Entering directory '/build/staden-2.0.0+b11/seq_utils' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss2.o -c align_ss2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_sv.o -c align_sv.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dna_utils.o -c dna_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c sequence_formats.c: In function 'get_embl_format_seq': sequence_formats.c:729:29: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 729 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:33: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 738 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function 'add_feat': sequence_formats.c:481:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 481 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 510 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib.o -c align_lib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.c renz_utils.c: In function 'SetREnzColour': renz_utils.c:1049:35: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 1049 | sprintf(colour, "#%02x%02x%02x", r, g, b); | ^ In file included from /usr/include/stdio.h:906, from renz_utils.c:3: In function 'sprintf', inlined from 'SetREnzColour' at renz_utils.c:1049:5: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 26 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin all cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip all cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all make[2]: Entering directory '/build/staden-2.0.0+b11/mutlib' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip all make[2]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/spin' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/screen_seq' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/qclip' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops all make[2]: Entering directory '/build/staden-2.0.0+b11/stops' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./vector_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./screen_seq -I/build/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./stops -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qclip.o -c qclip.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp seq_reg_cmds.c: In function 'GetActiveSeqName': seq_reg_cmds.c:919:32: warning: zero-length gnu_printf format string [-Wformat-zero-length] 919 | vTcl_SetResult(interp, ""); | ^~ g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c make[2]: Leaving directory '/build/staden-2.0.0+b11/stops' make[2]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all make[2]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all make[2]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./make_weights -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./find_renz -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedUtils.o -c tkSeqedUtils.c make[2]: Leaving directory '/build/staden-2.0.0+b11/qclip' cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 all make[2]: Entering directory '/build/staden-2.0.0+b11/gap5' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o screen_seq screen_seq.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp make[2]: Leaving directory '/build/staden-2.0.0+b11/find_renz' g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqedInterface.o -c seqedInterface.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp make[2]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c make[2]: Leaving directory '/build/staden-2.0.0+b11/make_weights' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c sp_alignment.cpp: In function 'void sp::store_hashn(Hash*)': sp_alignment.cpp:754:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ emboss_input_funcs.c: In function 'read_emboss_data_file': emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 402 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 444 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 477 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function 'init_emboss_stick_create': emboss_input_funcs.c:658:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 658 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 659 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpam.o -c readpam.c sp_hash_lib.cpp: In function 'int sp::hash_word8n(char*, int*, int, int, short unsigned int*)': sp_hash_lib.cpp:57:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 57 | register int i; | ^ sp_hash_lib.cpp:58:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:58:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:58:38: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:59:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 59 | register int unsigned short luword; | ^~~~~~ sp_hash_lib.cpp: In function 'int sp::hash_seq8n(char*, int*, int, int)': sp_hash_lib.cpp:99:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp: In function 'int sp::hash_word4n(char*, int*, int, int, unsigned char*)': sp_hash_lib.cpp:156:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 156 | register int i; | ^ sp_hash_lib.cpp:157:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:157:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:157:38: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:158:28: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 158 | register char unsigned luword; | ^~~~~~ sp_hash_lib.cpp: In function 'int sp::hash_seq4n(char*, int*, int, int)': sp_hash_lib.cpp:197:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp:197:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp:197:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c sp_hash_lib.cpp: In function 'void sp::remdup(int*, int*, int*, int*)': sp_hash_lib.cpp:411:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 411 | register int i; | ^ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:316:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 316 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from /build/staden-2.0.0+b11/./tk_utils/tkRaster.h:9, from seq_reg.h:6, from sequence_pair_display.c:4: In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:316:2: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:344:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 344 | sprintf(tmp, "%10d", i*10); | ^ In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:344:2: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_similar_spans.o -c sip_similar_spans.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_globals.o -c sip_globals.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probs.o -c probs.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sim.o -c sim.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_cache.o -c tracealign_cache.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c make[2]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libspin.so seq_reg.o seq_reg_cmds.o raster_cmds.o seq_raster.o sequtils.o seq_results.o seq_sendto.o spin_globals.o seq_plot_funcs.o seqed.o tkSeqed.o tkSeqedUtils.o tkSeqedNames.o seqed_write.o seqedInterface.o seqed_translate.o seqed_restriction_enzymes.o seqed_search.o sequence_pair_display.o emboss_input_funcs.o readpam.o compare_spans.o sip_hash.o sip_similar_spans.o sip_find_identity.o sip_quick_scan.o sip_align.o sip_globals.o sip_cmds.o sip_results.o rescan_matches.o probs.o sim.o sip_sim.o init.o nip_globals.o nip_cmds.o nip_base_comp.o nip_gene_search.o nip_trna_search.o codon_content.o nip_stop_codon.o trna_search.o splice_search.o nip_splice_search.o nip_string_search.o nip_wtmatrix_search.o nip_restriction_enzymes.o nip_canvas_box.o dinuc_freqs.o -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c make[2]: Leaving directory '/build/staden-2.0.0+b11/spin' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c cp /build/staden-2.0.0+b11/./mutlib/mutlib.def 2>&- make[2]: [/build/staden-2.0.0+b11/./mutlib/Makefile:81: /build/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libmutlib.so align.o basecall.o caller.o caller_snr.o caller_base.o caller_level.o dnatable.o muttag.o mutationtag.o mutationtag_utils.o pathutil.o peakcall.o stringlist.o tagarray.o trace.o validate.o read_matrix.o sp_align_lib.o sp_alignment.o sp_hash_lib.o sp_matrix.o tracediff.o tracediff_helper.o tracediff_mutations.o tracediff_parameters.o tracediff_validate.o tracealign.o tracealign_cache.o tracealign_helper.o tracealign_interpolate.o tracealign_preprocess.o tracealign_validate.o mutscan.o mutscan_helper.o mutscan_validate.o mutscan_analysis.o mutscan_preprocess.o mutscan_parameters.o -lseq_utils -ltk_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c make[2]: Leaving directory '/build/staden-2.0.0+b11/mutlib' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all make[2]: Entering directory '/build/staden-2.0.0+b11/gap4' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all make[2]: Entering directory '/build/staden-2.0.0+b11/tracediff' make[2]: warning: -j7 forced in submake: resetting jobserver mode. cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan all make[2]: Entering directory '/build/staden-2.0.0+b11/mutscan' make[2]: warning: -j7 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tracediff -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gap_range.c: In function 'gap_range_x': gap_range.c:310:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 310 | if (!HashTableSearch(lib_recs, (char *)r->library_rec, | ^ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c actf.c: In function 'actf_lock': actf.c:246:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 246 | write(fd, db_path, strlen(db_path)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c template_display.c: In function 'configure_template': template_display.c:374:41: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 374 | HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); | ^ g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c make[2]: Leaving directory '/build/staden-2.0.0+b11/tracediff' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c make[2]: Leaving directory '/build/staden-2.0.0+b11/mutscan' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c find_oligo.c: In function 'StringMatch': find_oligo.c:957:40: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ find_oligo.c:957:41: note: format string is defined here 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ In file included from /usr/include/stdio.h:906, from /build/staden-2.0.0+b11/./gap5/hache_table.h:5, from /build/staden-2.0.0+b11/./gap5/g-struct.h:24, from /build/staden-2.0.0+b11/./gap5/g.h:1, from tg_struct.h:4, from tg_gio.h:4, from io_utils.h:6, from find_oligo.c:4: In function 'sprintf', inlined from 'StringMatch' at find_oligo.c:957:4: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o preass.o -c preass.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list.o -c list.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probe.o -c probe.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template.o -c template.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash.o -c hash.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c readpair.c: In function 'readpair_obj_func': readpair.c:175:57: warning: '%s' directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", | ^~ 176 | *handle, c_list); | ~~~~~~ In file included from /usr/include/stdio.h:906, from readpair.c:18: In function 'sprintf', inlined from 'readpair_obj_func' at readpair.c:175:3: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 27 and 1060 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c tman_display.c: In function 'repositionSeq': tman_display.c:279:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:279:18: note: assuming directive output of 12 bytes 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: In function 'sprintf', inlined from 'repositionSeq' at tman_display.c:279:5: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c template_display.c: In function 'template_callback': template_display.c:2354:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, | ^~ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from template_display.c:2: In function 'sprintf', inlined from 'template_callback' at template_display.c:2354:3: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c copy_db.c: In function 'copy_read_name': copy_db.c:118:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 118 | sprintf(num, "#%d", iter++); | ^~ copy_db.c:118:30: note: directive argument in the range [1, 2147483646] 118 | sprintf(num, "#%d", iter++); | ^~~~~ In file included from /usr/include/stdio.h:906, from copy_db.c:1: In function 'sprintf', inlined from 'copy_read_name' at copy_db.c:118:3: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clip.o -c clip.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libgap5.so -L/build/staden-2.0.0+b11/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/./gap5/tg_index_common.c:105: warning: the use of `tmpnam' is dangerous, better use `mkstemp' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c notes.c: In function 'time_t2str': notes.c:829:21: warning: ' (' directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 829 | sprintf(buf, "%s (%ld)", buf2, (long)t); | ^~ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from notes.c:11: In function 'sprintf', inlined from 'time_t2str' at notes.c:829:5: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c make[2]: Leaving directory '/build/staden-2.0.0+b11/gap5' consistency_display.c: In function 'consistency_callback': consistency_display.c:883:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 883 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, | ^~ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from consistency_display.c:1: In function 'sprintf', inlined from 'consistency_callback' at consistency_display.c:883:3: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o undo.o -c undo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: In function 'sprintf', inlined from 'repositionSeq' at tman_display.c:281:5: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o join.o -c join.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.c copy_db_main.c: In function 'main': copy_db_main.c:86:9: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o copy_db gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o copy_db.o copy_db_main.o text-io-reg.o io_utils.o io_handle.o -lg -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libgap.so -L/build/staden-2.0.0+b11/lib gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o IO2.o seqInfo.o parse_ft.o IO3.o io_utils.o io_handle.o gap-tcl.o tk-io-reg.o gap_cli_arg.o gap_globals.o newgap_cmds.o init.o consen.o gap_hash.o qual.o qualIO.o bubbl3.o tagdb.o notedb.o active_tags.o dbcheck.o clones.o extract.o preass.o list.o reactions.o probe.o template.o template_display.o ruler_display.o gap_canvas_box.o hash.o gap_array.o show_relationships.o fij.o hash_lib.o do_fij.o auto_assemble.o dis_readings.o find_repeats.o break_contig.o quality_plot.o readpair.o contig_selector.o complement.o cs-object.o list_proc.o dstrand.o oligo_sel.o primlib.o alter_rel.o restriction_enzymes.o stop_codon.o assemble_direct.o check_assembly.o tagU2.o mess.o find_oligo.o copy_db.o contig_order.o clip.o notes.o consistency_display.o consistency_canvas_box.o confidence_graph.o reading_coverage.o readpair_coverage.o strand_coverage.o find_fragments.o vseqs.o legacy_f2c.o f2c.o shuffle_pads.o auto_break.o tkEditor.o tkEdNames.o tkEdUtils.o edInterface.o edUtils2.o tagU1.o undo.o edExtend.o edCommands.o edMutations.o tagEditor.o searchUtils.o tman_interface.o tman_display.o tman_cons.o tman_diff.o contigEditor.o join.o oligo.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert all make[2]: Entering directory '/build/staden-2.0.0+b11/prefinish' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/haplo' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/copy_reads' make[2]: warning: -j7 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/convert' make[2]: warning: -j7 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish.o -c finish.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c main.c: In function 'get_db': main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o process.o -c process.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_filter.o -c finish_filter.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c copy_reads.c: In function 'create_si_struct': copy_reads.c:125:26: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 125 | sprintf(comment, "%s %s", tag_text, io_name(io)); | ^~ In file included from /usr/include/stdio.h:906, from copy_reads.c:4: In function 'sprintf', inlined from 'create_si_struct' at copy_reads.c:125:5: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ copy_reads.c: In function 'copy_reads': copy_reads.c:409:34: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); | ^~ In function 'sprintf', inlined from 'copy_reads' at copy_reads.c:409:6: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/staden-2.0.0+b11/convert' gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libprefinish.so finish.o finish_hash.o finish_long.o finish_main.o finish_utils.o finish_walk.o finish_reverse.o finish_filter.o finish_pcr.o dust.o -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 make[2]: Leaving directory '/build/staden-2.0.0+b11/prefinish' make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/staden-2.0.0+b11' dh_auto_install make -j7 install DESTDIR=/build/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/staden-2.0.0+b11' mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/bin mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/doc mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/man cp shlib.conf /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp ./staden.profile /build/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/staden-2.0.0+b11' cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc install cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev install cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install make[4]: Entering directory '/build/staden-2.0.0+b11/Misc' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install make[4]: Entering directory '/build/staden-2.0.0+b11/trev' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/primer3' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts install make[4]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/scripts' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libmisc.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/Misc' install trev /build/staden-2.0.0+b11/debian/tmp/usr/bin /build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3' cp /build/staden-2.0.0+b11/lib/libprimer3.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data install cp /build/staden-2.0.0+b11/./trev/trev.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev /build/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' cp /build/staden-2.0.0+b11/./trev/trevrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install cp /build/staden-2.0.0+b11/./spin_emboss/*.tcl /build/staden-2.0.0+b11/./spin_emboss/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss make[4]: Leaving directory '/build/staden-2.0.0+b11/trev' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 cp /build/staden-2.0.0+b11/./pregap4/*.tcl /build/staden-2.0.0+b11/./pregap4/widget_licence /build/staden-2.0.0+b11/./pregap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 make[4]: Entering directory '/build/staden-2.0.0+b11/data' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./scripts/assemble4 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install cp /build/staden-2.0.0+b11/./scripts/fasta-split /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi install cp /build/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/staden-2.0.0+b11/text_utils' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./scripts/splitseq_da /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts /build/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' make[4]: Entering directory '/build/staden-2.0.0+b11/abi' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./scripts/staden_help /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Leaving directory '/build/staden-2.0.0+b11/scripts' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf install cp /build/staden-2.0.0+b11/./data/alus/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libtk_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Entering directory '/build/staden-2.0.0+b11/alf' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/text_utils' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-2.0.0+b11/./tk_utils/*.tcl /build/staden-2.0.0+b11/./tk_utils/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cp getABISampleName getABIcomment getABIdate getABIfield /build/staden-2.0.0+b11/debian/tmp/usr/bin cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g install cp: cannot stat '/build/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory make[4]: [/build/staden-2.0.0+b11/./spin_emboss/Makefile:30: install] Error 1 (ignored) cp /build/staden-2.0.0+b11/./spin_emboss/emboss_menu /build/staden-2.0.0+b11/./spin_emboss/spin_embossrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' make[4]: Leaving directory '/build/staden-2.0.0+b11/abi' make[4]: Entering directory '/build/staden-2.0.0+b11/g' make[4]: warning: -j7 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/eba' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/alf' cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field install cp /build/staden-2.0.0+b11/lib/libg.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/g' cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins install make[4]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp init_exp /build/staden-2.0.0+b11/debian/tmp/usr/bin cp eba /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/init_exp' make[4]: Entering directory '/build/staden-2.0.0+b11/hetins' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/eba' cp get_scf_field /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' cp hetins /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/hetins' cp /build/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates cp: cannot stat '/build/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory make[4]: [/build/staden-2.0.0+b11/./pregap4/Makefile:42: install] Error 1 (ignored) cp /build/staden-2.0.0+b11/./pregap4/naming_schemes/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-2.0.0+b11/./tk_utils/stash /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./tk_utils/2bars_*.bmp /build/staden-2.0.0+b11/./tk_utils/help_config /build/staden-2.0.0+b11/./tk_utils/tk_utilsrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./pregap4/pregap4rc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/pregap4' make[4]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' make[4]: warning: -j7 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cp /build/staden-2.0.0+b11/./data/blast_data/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cp /build/staden-2.0.0+b11/lib/libseq_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-2.0.0+b11/./data/gcodes/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib install cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin install cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip install make[4]: Entering directory '/build/staden-2.0.0+b11/mutlib' cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/screen_seq' make[4]: warning: -j7 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors cp /build/staden-2.0.0+b11/./data/vectors/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors make[4]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/qclip' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp vector_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libmutlib.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden install spin /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' make[4]: Leaving directory '/build/staden-2.0.0+b11/mutlib' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin cp screen_seq /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./spin/*.tcl /build/staden-2.0.0+b11/./spin/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops install cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install cp polyA_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' make[4]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' cp /build/staden-2.0.0+b11/./data/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/stops' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install make[4]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/mutscan' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./data/renzyme_bairoch /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./data/m13mp18_primers /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp make_weights /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./data/vector_primer /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/stops' make[4]: Leaving directory '/build/staden-2.0.0+b11/make_weights' cp /build/staden-2.0.0+b11/./data/pam250 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/data' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install cp mutscan /build/staden-2.0.0+b11/debian/tmp/usr/bin cp find_renz /build/staden-2.0.0+b11/debian/tmp/usr/bin install gap5 /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/mutscan' make[4]: Leaving directory '/build/staden-2.0.0+b11/find_renz' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp /build/staden-2.0.0+b11/./gap5/*.tcl /build/staden-2.0.0+b11/./gap5/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 make[4]: Entering directory '/build/staden-2.0.0+b11/gap4' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/tracediff' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp tracediff /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/tracediff' cp /build/staden-2.0.0+b11/./spin/*.wts /build/staden-2.0.0+b11/./spin/niprc /build/staden-2.0.0+b11/./spin/siprc /build/staden-2.0.0+b11/./spin/spinrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap5/../gap4/acd2tag.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 make[4]: Leaving directory '/build/staden-2.0.0+b11/spin' cp /build/staden-2.0.0+b11/./gap5/gap5rc /build/staden-2.0.0+b11/./gap5/gap5rc_menu_full /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/lib/libgap5.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp copy_db /build/staden-2.0.0+b11/debian/tmp/usr/bin cp tg_index.bin /build/staden-2.0.0+b11/debian/tmp/usr/bin install gap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp /build/staden-2.0.0+b11/./gap4/*.tcl /build/staden-2.0.0+b11/./gap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap install tg_index /build/staden-2.0.0+b11/debian/tmp/usr/bin install gap5_cmd /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/gap5' cp /build/staden-2.0.0+b11/lib/libgap.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/./gap4/gaprc /build/staden-2.0.0+b11/./gap4/gaprc_menu_full /build/staden-2.0.0+b11/./gap4/gaprc_menu_mito /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/GTAGDB /build/staden-2.0.0+b11/./gap4/NOTEDB /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/cap2rc /build/staden-2.0.0+b11/./gap4/cap3rc /build/staden-2.0.0+b11/./gap4/fak2rc /build/staden-2.0.0+b11/./gap4/phraprc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/*.bitmap /build/staden-2.0.0+b11/./gap4/*.gif /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install make[4]: Entering directory '/build/staden-2.0.0+b11/prefinish' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo install cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install make[4]: Entering directory '/build/staden-2.0.0+b11/haplo' make[4]: warning: -j7 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/copy_reads' make[4]: warning: -j7 forced in submake: resetting jobserver mode. cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j7 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert install make[4]: Entering directory '/build/staden-2.0.0+b11/convert' make[4]: warning: -j7 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-2.0.0+b11/./haplo/*.tcl /build/staden-2.0.0+b11/./haplo/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo cp /build/staden-2.0.0+b11/./prefinish/*.tcl /build/staden-2.0.0+b11/./prefinish/*.itcl /build/staden-2.0.0+b11/./prefinish/*.itk /build/staden-2.0.0+b11/./prefinish/help /build/staden-2.0.0+b11/./prefinish/args.template /build/staden-2.0.0+b11/./prefinish/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-2.0.0+b11/lib/libhaplo.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads install copy_reads /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./haplo/haplorc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/staden-2.0.0+b11/./copy_reads/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads make[4]: Leaving directory '/build/staden-2.0.0+b11/haplo' cp staden_convert /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libcopy_reads.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/convert' cp /build/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-2.0.0+b11/lib/libprefinish.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' install prefinish /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./prefinish/finish_sanger /build/staden-2.0.0+b11/./prefinish/finish_cDNA /build/staden-2.0.0+b11/./prefinish/finish_cDNA_ends_only \ /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-2.0.0+b11/./prefinish/rules/*.rule /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-2.0.0+b11/./prefinish/prefinishrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/prefinish' make[3]: Leaving directory '/build/staden-2.0.0+b11' make[2]: Leaving directory '/build/staden-2.0.0+b11' # Remove file causing lintian errors that is targeting at windows find debian -name help_windows.tcl -delete # Remove some empty directories find debian -type d -empty -name acdtcl -delete find debian -type d -empty -name templates -delete # Build system is not prepared for multi-arch mv /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/* /build/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4_i386.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_i386.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-4_all.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-4_i386.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-4_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/19802/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/19802/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/19802 and its subdirectories I: Current time: Wed Apr 19 18:55:28 +14 2023 I: pbuilder-time-stamp: 1681880128