I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 26 04:51:35 -12 2020 I: pbuilder-time-stamp: 1603731095 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: 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: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 12 00:48:12 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./staden_2.0.0+b11-4.dsc 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/14608/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='892f4efb1f2e473ea14f5ca70ee8a68c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='14608' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ADAtiO3g8s/pbuilderrc_9Iii --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ADAtiO3g8s/b1 --logfile b1/build.log staden_2.0.0+b11-4.dsc' SUDO_GID='115' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux p64c 4.19.0-12-arm64 #1 SMP Debian 4.19.152-1 (2020-10-18) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 20 20:31 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/14608/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team 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 ... 18932 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} bsdmainutils{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} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype6{a} libfreetype6-dev{a} libglib2.0-0{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpng-dev{a} libpng16-16{a} libpsl5{a} libpthread-stubs0-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm-dev{a} libsm6{a} libssh2-1{a} libssl1.1{a} libstaden-read-dev{a} libstaden-read13{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} libxt-dev{a} libxt6{a} lsb-base{a} m4{a} man-db{a} pkg-config{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} ucf{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} x11proto-scrnsaver-dev{a} x11proto-xext-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 deepin-terminal eterm gnome-terminal kitty konsole krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules lilyterm lxterminal lynx mate-terminal mlterm mlterm-tiny pterm publicsuffix qterminal rxvt-unicode sakura shared-mime-info stterm tcllib terminator terminology termit tilix wget xdg-user-dirs xfce4-terminal xiterm+thai xterm 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 36.3 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1+deb10u1 [698 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libtcl8.6 armhf 8.6.9+dfsg-2 [897 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 16 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 17 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 18 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 19 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libxft2 armhf 2.3.2-2 [50.1 kB] Get: 24 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 25 http://deb.debian.org/debian buster/main armhf x11-common all 1:7.7+19 [251 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libtk8.6 armhf 8.6.9-2 [678 kB] Get: 28 http://deb.debian.org/debian buster/main armhf itcl3 armhf 3.4.3-3 [44.3 kB] Get: 29 http://deb.debian.org/debian buster/main armhf itk3 armhf 3.4.2-3 [26.3 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 32 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 33 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 35 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 36 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 37 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 38 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 39 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 41 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 44 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 46 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 52 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 53 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 54 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 55 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 56 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 57 http://deb.debian.org/debian buster/main armhf tcl8.6 armhf 8.6.9+dfsg-2 [123 kB] Get: 58 http://deb.debian.org/debian buster/main armhf tcl8.6-dev armhf 8.6.9+dfsg-2 [917 kB] Get: 59 http://deb.debian.org/debian buster/main armhf tcl armhf 8.6.9+1 [5636 B] Get: 60 http://deb.debian.org/debian buster/main armhf tcl-dev armhf 8.6.9+1 [8192 B] Get: 61 http://deb.debian.org/debian buster/main armhf itcl3-dev armhf 3.4.3-3 [15.5 kB] Get: 62 http://deb.debian.org/debian buster/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get: 63 http://deb.debian.org/debian buster/main armhf x11proto-dev all 2018.4-4 [251 kB] Get: 64 http://deb.debian.org/debian buster/main armhf x11proto-core-dev all 2018.4-4 [3128 B] Get: 65 http://deb.debian.org/debian buster/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.5 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.7 kB] Get: 67 http://deb.debian.org/debian buster/main armhf xtrans-dev all 1.3.5-1 [100 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B] Get: 69 http://deb.debian.org/debian buster/main armhf libxcb1-dev armhf 1.13.1-2 [171 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libx11-dev armhf 2:1.6.7-1+deb10u1 [770 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libice6 armhf 2:1.0.9-2 [51.7 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libxt6 armhf 1:1.1.5-1+b3 [159 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libice-dev armhf 2:1.0.9-2 [61.9 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libsm-dev armhf 2:1.2.3-1 [36.1 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libxt-dev armhf 1:1.1.5-1+b3 [403 kB] Get: 77 http://deb.debian.org/debian buster/main armhf x11proto-xext-dev all 2018.4-4 [3128 B] Get: 78 http://deb.debian.org/debian buster/main armhf libxext-dev armhf 2:1.3.3-1+b2 [103 kB] Get: 79 http://deb.debian.org/debian buster/main armhf x11proto-scrnsaver-dev all 2018.4-4 [3136 B] Get: 80 http://deb.debian.org/debian buster/main armhf libxss-dev armhf 1:1.2.3-1 [23.1 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libpng-dev armhf 1.6.36-6 [286 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libfreetype6-dev armhf 2.9.1-3+deb10u1 [491 kB] Get: 84 http://deb.debian.org/debian buster/main armhf uuid-dev armhf 2.33.1-0.1 [92.6 kB] Get: 85 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libfontconfig1-dev armhf 2.13.1-2 [950 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libxrender-dev armhf 1:0.9.10-1 [37.8 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libxft-dev armhf 2.3.2-2 [62.3 kB] Get: 89 http://deb.debian.org/debian buster/main armhf tk8.6 armhf 8.6.9-2 [71.9 kB] Get: 90 http://deb.debian.org/debian buster/main armhf tk8.6-dev armhf 8.6.9-2 [694 kB] Get: 91 http://deb.debian.org/debian buster/main armhf tk armhf 8.6.9+1 [5676 B] Get: 92 http://deb.debian.org/debian buster/main armhf tk-dev armhf 8.6.9+1 [5500 B] Get: 93 http://deb.debian.org/debian buster/main armhf itk3-dev armhf 3.4.2-3 [5492 B] Get: 94 http://deb.debian.org/debian buster/main armhf iwidgets4 all 4.1.1-2 [210 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [28.8 kB] Get: 96 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 97 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 101 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 102 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 103 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 104 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 105 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 106 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 107 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 108 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 109 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 110 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB] Get: 111 http://deb.debian.org/debian buster/main armhf libcurl4-gnutls-dev armhf 7.64.0-4+deb10u1 [389 kB] Get: 112 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 113 http://deb.debian.org/debian buster/main armhf libncurses-dev armhf 6.1+20181013-2+deb10u2 [295 kB] Get: 114 http://deb.debian.org/debian buster/main armhf libncurses5-dev armhf 6.1+20181013-2+deb10u2 [948 B] Get: 115 http://deb.debian.org/debian buster/main armhf libstaden-read13 armhf 1.14.11-6 [251 kB] Get: 116 http://deb.debian.org/debian buster/main armhf libstaden-read-dev armhf 1.14.11-6 [331 kB] Get: 117 http://deb.debian.org/debian buster/main armhf tklib all 0.6+20190108-1 [1220 kB] Fetched 36.3 MB in 7s (5155 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../002-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../004-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../006-libxau6_1%3a1.0.8-1+b2_armhf.deb ... Unpacking libxau6:armhf (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../007-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../008-libxcb1_1.13.1-2_armhf.deb ... Unpacking libxcb1:armhf (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../009-libx11-data_2%3a1.6.7-1+deb10u1_all.deb ... Unpacking libx11-data (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../010-libx11-6_2%3a1.6.7-1+deb10u1_armhf.deb ... Unpacking libx11-6:armhf (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libtcl8.6:armhf. Preparing to unpack .../011-libtcl8.6_8.6.9+dfsg-2_armhf.deb ... Unpacking libtcl8.6:armhf (8.6.9+dfsg-2) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../012-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../013-libpng16-16_1.6.36-6_armhf.deb ... Unpacking libpng16-16:armhf (1.6.36-6) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../014-libfreetype6_2.9.1-3+deb10u1_armhf.deb ... Unpacking libfreetype6:armhf (2.9.1-3+deb10u1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../015-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../017-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../018-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../019-libfontconfig1_2.13.1-2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-2) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../020-libxext6_2%3a1.3.3-1+b2_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1+b2) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../021-libxrender1_1%3a0.9.10-1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1) ... Selecting previously unselected package libxft2:armhf. Preparing to unpack .../022-libxft2_2.3.2-2_armhf.deb ... Unpacking libxft2:armhf (2.3.2-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../023-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package x11-common. Preparing to unpack .../024-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxss1:armhf. Preparing to unpack .../025-libxss1_1%3a1.2.3-1_armhf.deb ... Unpacking libxss1:armhf (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:armhf. Preparing to unpack .../026-libtk8.6_8.6.9-2_armhf.deb ... Unpacking libtk8.6:armhf (8.6.9-2) ... Selecting previously unselected package itcl3:armhf. Preparing to unpack .../027-itcl3_3.4.3-3_armhf.deb ... Unpacking itcl3:armhf (3.4.3-3) ... Selecting previously unselected package itk3:armhf. Preparing to unpack .../028-itk3_3.4.2-3_armhf.deb ... Unpacking itk3:armhf (3.4.2-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../029-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../030-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../031-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../032-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../033-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../034-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../035-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../036-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../037-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../038-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../039-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../040-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../041-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../042-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../043-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../044-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../045-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../046-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../047-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../048-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../049-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../050-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../053-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../055-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../056-tcl8.6_8.6.9+dfsg-2_armhf.deb ... Unpacking tcl8.6 (8.6.9+dfsg-2) ... Selecting previously unselected package tcl8.6-dev:armhf. Preparing to unpack .../057-tcl8.6-dev_8.6.9+dfsg-2_armhf.deb ... Unpacking tcl8.6-dev:armhf (8.6.9+dfsg-2) ... Selecting previously unselected package tcl. Preparing to unpack .../058-tcl_8.6.9+1_armhf.deb ... Unpacking tcl (8.6.9+1) ... Selecting previously unselected package tcl-dev:armhf. Preparing to unpack .../059-tcl-dev_8.6.9+1_armhf.deb ... Unpacking tcl-dev:armhf (8.6.9+1) ... Selecting previously unselected package itcl3-dev:armhf. Preparing to unpack .../060-itcl3-dev_3.4.3-3_armhf.deb ... Unpacking itcl3-dev:armhf (3.4.3-3) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../061-xorg-sgml-doctools_1%3a1.11-1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../062-x11proto-dev_2018.4-4_all.deb ... Unpacking x11proto-dev (2018.4-4) ... Selecting previously unselected package x11proto-core-dev. Preparing to unpack .../063-x11proto-core-dev_2018.4-4_all.deb ... Unpacking x11proto-core-dev (2018.4-4) ... Selecting previously unselected package libxau-dev:armhf. Preparing to unpack .../064-libxau-dev_1%3a1.0.8-1+b2_armhf.deb ... Unpacking libxau-dev:armhf (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp-dev:armhf. Preparing to unpack .../065-libxdmcp-dev_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp-dev:armhf (1:1.1.2-3) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../066-xtrans-dev_1.3.5-1_all.deb ... Unpacking xtrans-dev (1.3.5-1) ... Selecting previously unselected package libpthread-stubs0-dev:armhf. Preparing to unpack .../067-libpthread-stubs0-dev_0.4-1_armhf.deb ... Unpacking libpthread-stubs0-dev:armhf (0.4-1) ... Selecting previously unselected package libxcb1-dev:armhf. Preparing to unpack .../068-libxcb1-dev_1.13.1-2_armhf.deb ... Unpacking libxcb1-dev:armhf (1.13.1-2) ... Selecting previously unselected package libx11-dev:armhf. Preparing to unpack .../069-libx11-dev_2%3a1.6.7-1+deb10u1_armhf.deb ... Unpacking libx11-dev:armhf (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libice6:armhf. Preparing to unpack .../070-libice6_2%3a1.0.9-2_armhf.deb ... Unpacking libice6:armhf (2:1.0.9-2) ... Selecting previously unselected package libsm6:armhf. Preparing to unpack .../071-libsm6_2%3a1.2.3-1_armhf.deb ... Unpacking libsm6:armhf (2:1.2.3-1) ... Selecting previously unselected package libxt6:armhf. Preparing to unpack .../072-libxt6_1%3a1.1.5-1+b3_armhf.deb ... Unpacking libxt6:armhf (1:1.1.5-1+b3) ... Selecting previously unselected package libice-dev:armhf. Preparing to unpack .../073-libice-dev_2%3a1.0.9-2_armhf.deb ... Unpacking libice-dev:armhf (2:1.0.9-2) ... Selecting previously unselected package libsm-dev:armhf. Preparing to unpack .../074-libsm-dev_2%3a1.2.3-1_armhf.deb ... Unpacking libsm-dev:armhf (2:1.2.3-1) ... Selecting previously unselected package libxt-dev:armhf. Preparing to unpack .../075-libxt-dev_1%3a1.1.5-1+b3_armhf.deb ... Unpacking libxt-dev:armhf (1:1.1.5-1+b3) ... Selecting previously unselected package x11proto-xext-dev. Preparing to unpack .../076-x11proto-xext-dev_2018.4-4_all.deb ... Unpacking x11proto-xext-dev (2018.4-4) ... Selecting previously unselected package libxext-dev:armhf. Preparing to unpack .../077-libxext-dev_2%3a1.3.3-1+b2_armhf.deb ... Unpacking libxext-dev:armhf (2:1.3.3-1+b2) ... Selecting previously unselected package x11proto-scrnsaver-dev. Preparing to unpack .../078-x11proto-scrnsaver-dev_2018.4-4_all.deb ... Unpacking x11proto-scrnsaver-dev (2018.4-4) ... Selecting previously unselected package libxss-dev:armhf. Preparing to unpack .../079-libxss-dev_1%3a1.2.3-1_armhf.deb ... Unpacking libxss-dev:armhf (1:1.2.3-1) ... Selecting previously unselected package libexpat1-dev:armhf. Preparing to unpack .../080-libexpat1-dev_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1-dev:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package libpng-dev:armhf. Preparing to unpack .../081-libpng-dev_1.6.36-6_armhf.deb ... Unpacking libpng-dev:armhf (1.6.36-6) ... Selecting previously unselected package libfreetype6-dev:armhf. Preparing to unpack .../082-libfreetype6-dev_2.9.1-3+deb10u1_armhf.deb ... Unpacking libfreetype6-dev:armhf (2.9.1-3+deb10u1) ... Selecting previously unselected package uuid-dev:armhf. Preparing to unpack .../083-uuid-dev_2.33.1-0.1_armhf.deb ... Unpacking uuid-dev:armhf (2.33.1-0.1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../084-pkg-config_0.29-6_armhf.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package libfontconfig1-dev:armhf. Preparing to unpack .../085-libfontconfig1-dev_2.13.1-2_armhf.deb ... Unpacking libfontconfig1-dev:armhf (2.13.1-2) ... Selecting previously unselected package libxrender-dev:armhf. Preparing to unpack .../086-libxrender-dev_1%3a0.9.10-1_armhf.deb ... Unpacking libxrender-dev:armhf (1:0.9.10-1) ... Selecting previously unselected package libxft-dev:armhf. Preparing to unpack .../087-libxft-dev_2.3.2-2_armhf.deb ... Unpacking libxft-dev:armhf (2.3.2-2) ... Selecting previously unselected package tk8.6. Preparing to unpack .../088-tk8.6_8.6.9-2_armhf.deb ... Unpacking tk8.6 (8.6.9-2) ... Selecting previously unselected package tk8.6-dev:armhf. Preparing to unpack .../089-tk8.6-dev_8.6.9-2_armhf.deb ... Unpacking tk8.6-dev:armhf (8.6.9-2) ... Selecting previously unselected package tk. Preparing to unpack .../090-tk_8.6.9+1_armhf.deb ... Unpacking tk (8.6.9+1) ... Selecting previously unselected package tk-dev:armhf. Preparing to unpack .../091-tk-dev_8.6.9+1_armhf.deb ... Unpacking tk-dev:armhf (8.6.9+1) ... Selecting previously unselected package itk3-dev:armhf. Preparing to unpack .../092-itk3-dev_3.4.2-3_armhf.deb ... Unpacking itk3-dev:armhf (3.4.2-3) ... Selecting previously unselected package iwidgets4. Preparing to unpack .../093-iwidgets4_4.1.1-2_all.deb ... Unpacking iwidgets4 (4.1.1-2) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../094-libbz2-dev_1.0.6-9.2~deb10u1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../095-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../096-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../097-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../098-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../099-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../100-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../101-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../102-libsasl2-2_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../103-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../104-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../105-libnghttp2-14_1.36.0-2+deb10u1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../106-libpsl5_0.20.2-2_armhf.deb ... Unpacking libpsl5:armhf (0.20.2-2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../107-librtmp1_2.4+20151223.gitfa8646d.1-2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../108-libssh2-1_1.8.0-2.1_armhf.deb ... Unpacking libssh2-1:armhf (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../109-libcurl3-gnutls_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../110-libcurl4-gnutls-dev_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../111-liblzma-dev_5.2.4-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.4-1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../112-libncurses-dev_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses-dev:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../113-libncurses5-dev_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses5-dev:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libstaden-read13:armhf. Preparing to unpack .../114-libstaden-read13_1.14.11-6_armhf.deb ... Unpacking libstaden-read13:armhf (1.14.11-6) ... Selecting previously unselected package libstaden-read-dev. Preparing to unpack .../115-libstaden-read-dev_1.14.11-6_armhf.deb ... Unpacking libstaden-read-dev (1.14.11-6) ... Selecting previously unselected package tklib. Preparing to unpack .../116-tklib_0.6+20190108-1_all.deb ... Unpacking tklib (0.6+20190108-1) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up lsb-base (10.2019051400) ... Setting up libxau6:armhf (1:1.0.8-1+b2) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up libpsl5:armhf (0.20.2-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libpthread-stubs0-dev:armhf (0.4-1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up xtrans-dev (1.3.5-1) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:armhf (2.2.6-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up uuid-dev:armhf (2.33.1-0.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up libtcl8.6:armhf (8.6.9+dfsg-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Setting up x11proto-dev (2018.4-4) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:armhf (2:1.0.9-2) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up tcl8.6 (8.6.9+dfsg-2) ... Setting up libncurses-dev:armhf (6.1+20181013-2+deb10u2) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libxau-dev:armhf (1:1.0.8-1+b2) ... Setting up libice-dev:armhf (2:1.0.9-2) ... Setting up libtool (2.4.6-9) ... Setting up tcl8.6-dev:armhf (8.6.9+dfsg-2) ... Setting up libpng-dev:armhf (1.6.36-6) ... Setting up itcl3:armhf (3.4.3-3) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libxdmcp-dev:armhf (1:1.1.2-3) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up x11proto-xext-dev (2018.4-4) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up tcl (8.6.9+1) ... Setting up libncurses5-dev:armhf (6.1+20181013-2+deb10u2) ... Setting up libx11-6:armhf (2:1.6.7-1+deb10u1) ... Setting up x11proto-scrnsaver-dev (2018.4-4) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up itcl3-dev:armhf (3.4.3-3) ... Setting up libxcb1-dev:armhf (1.13.1-2) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libsm-dev:armhf (2:1.2.3-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libx11-dev:armhf (2:1.6.7-1+deb10u1) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Setting up libcurl4-gnutls-dev:armhf (7.64.0-4+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libfreetype6-dev:armhf (2.9.1-3+deb10u1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:armhf (1:1.1.5-1+b3) ... Setting up tcl-dev:armhf (8.6.9+1) ... Setting up libxext-dev:armhf (2:1.3.3-1+b2) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up libxrender-dev:armhf (1:0.9.10-1) ... Setting up libstaden-read13:armhf (1.14.11-6) ... Setting up libxft2:armhf (2.3.2-2) ... Setting up libfontconfig1-dev:armhf (2.13.1-2) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:armhf (8.6.9-2) ... Setting up libstaden-read-dev (1.14.11-6) ... Setting up libxss-dev:armhf (1:1.2.3-1) ... Setting up itk3:armhf (3.4.2-3) ... Setting up libxt-dev:armhf (1:1.1.5-1+b3) ... Setting up iwidgets4 (4.1.1-2) ... Setting up libxft-dev:armhf (2.3.2-2) ... Setting up tk8.6 (8.6.9-2) ... Setting up tk8.6-dev:armhf (8.6.9-2) ... Setting up tk (8.6.9+1) ... Setting up itk3-dev:armhf (3.4.2-3) ... Setting up tk-dev:armhf (8.6.9+1) ... Setting up tklib (0.6+20190108-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/staden-2.0.0+b11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b 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 armhf 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 aclocal: 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/arm-linux-gnueabihf \ --with-itk=/usr/lib/tcltk/arm-linux-gnueabihf ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-itcl=/usr/lib/tcltk/arm-linux-gnueabihf --with-itk=/usr/lib/tcltk/arm-linux-gnueabihf configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.64.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking png.h usability... yes checking png.h presence... 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 io_lib/Read.h usability... yes checking io_lib/Read.h presence... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking ncurses.h usability... yes checking ncurses.h presence... yes checking for ncurses.h... yes checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes checking pwd.h usability... yes checking pwd.h presence... 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 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... yes 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-4.19.0-12-arm64 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/tklib0.6) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/arm-linux-gnueabihf/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/arm-linux-gnueabihf/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 configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking ---------------------------------------------------------------------- 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/tklib0.6 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/arm-linux-gnueabihf/itcl3.4 Itk: /usr/lib/tcltk/arm-linux-gnueabihf/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_auto_build make -j3 make[1]: Entering directory '/build/staden-2.0.0+b11' cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev all cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc all make[2]: Entering directory '/build/staden-2.0.0+b11/trev' make[2]: warning: -j3 forced in submake: resetting jobserver mode. cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all make[2]: Entering directory '/build/staden-2.0.0+b11/Misc' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/primer3' make[2]: warning: -j3 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 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'. 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 make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/trev' cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j3 --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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all make[2]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[2]: warning: -j3 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' gcc -g -O2 -ffile-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 gcc -g -O2 -ffile-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 -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 Nothing to build for Pregap4. make[2]: Leaving directory '/build/staden-2.0.0+b11/pregap4' cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j3 --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/spin_emboss' make[2]: warning: -j3 forced in submake: resetting jobserver mode. /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' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 Nothing to build for spin_emboss. make[2]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j3 --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/scripts' make[2]: warning: -j3 forced in submake: resetting jobserver mode. /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' gcc -g -O2 -ffile-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 scripts. make[2]: Leaving directory '/build/staden-2.0.0+b11/scripts' cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j3 --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 find.o -c find.c make[2]: Entering directory '/build/staden-2.0.0+b11/data' make[2]: warning: -j3 forced in submake: resetting jobserver mode. /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' Nothing to build for data. make[2]: Leaving directory '/build/staden-2.0.0+b11/data' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -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 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 parse_db.c: In function 'parse_entry': parse_db.c:234:52: warning: '%s' directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); ^~ ~~~~ In file included from /usr/include/stdio.h:873, from parse_db.c:19: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 33 and 8224 bytes into a destination of size 8192 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 strtol64.o -c strtol64.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 boulder_input.o -c boulder_input.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 -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 -j3 --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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all make[2]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/text_utils' make[2]: warning: -j3 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/./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/./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/./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 -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 -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 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] write(2, pr_program_name, pr_program_name_len), \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' if (NULL == r) OOM_ERROR; ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' if (NULL == r) OOM_ERROR; ^~~~~~~~~ make[2]: Leaving directory '/build/staden-2.0.0+b11/text_utils' cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi all make[2]: Entering directory '/build/staden-2.0.0+b11/abi' make[2]: warning: -j3 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 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/./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/./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/./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/./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/./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/./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 primer3_main.c: In function 'boulder_print_oligos': primer3_main.c:416:25: warning: '%d' directive writing between 1 and 8 bytes into a region of size 2 [-Wformat-overflow=] else sprintf(suffix, "_%d", i); ^~ primer3_main.c:416:23: note: directive argument in the range [1, 53687092] else sprintf(suffix, "_%d", i); ^~~~~ In file included from /usr/include/stdio.h:873, from primer3_main.c:7: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 10 bytes into a destination of size 3 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c: In function 'main': primer3_main.c:234:25: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] else sprintf(suffix, "_%d", i); ^~ primer3_main.c:234:23: note: directive argument in the range [1, 2147483647] else sprintf(suffix, "_%d", i); ^~~~~ In file included from /usr/include/stdio.h:873, from primer3_main.c:7: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 misc.o -c misc.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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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/./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 -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 text_output.o -c text_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 -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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/abi' cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf all make[2]: Entering directory '/build/staden-2.0.0+b11/alf' make[2]: warning: -j3 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/./alf -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c alfsplit.c: In function 'main': alfsplit.c:347:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread (buf,512,1,inData) ; ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] fread (ent->label,40,1,fil) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:135:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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/./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 -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' cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j3 --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/g' make[2]: warning: -j3 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/./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/./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/./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/./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/./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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -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 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 make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j3 --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: -j3 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/./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/./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 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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -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/./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 tkTraceIO.o -c tkTraceIO.c make[2]: Leaving directory '/build/staden-2.0.0+b11/eba' cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j3 --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: -j3 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/./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 make[2]: Leaving directory '/build/staden-2.0.0+b11/g' cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j3 --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: -j3 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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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 get_scf_field get_scf_field.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc make[2]: Leaving directory '/build/staden-2.0.0+b11/init_exp' cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j3 --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: -j3 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/get_scf_field' tkTraceDisp.c: In function 'trace_draw_numbers': tkTraceDisp.c:746:25: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(number, "%d", cind); ^ In file included from /usr/include/stdio.h:873, from tkTraceDisp.c:2: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 capture.o -c capture.c capture.c: In function 'tcl_capture': capture.c:33:7: warning: implicit declaration of function 'mkostemp'; did you mean 'mkstemp'? [-Wimplicit-function-declaration] fd = mkostemp(NULL, 0666); ^~~~~~~~ mkstemp capture.c:54:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] 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 canvas_box.o -c 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/./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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm 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 restriction_enzyme_map.o -c restriction_enzyme_map.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -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 -j3 --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: -j3 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 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=] sprintf(colour, "#%02x%02x%02x", r, g, b); ^ In file included from /usr/include/stdio.h:873, from renz_utils.c:3: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 26 bytes into a destination of size 7 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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/./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 sequence_formats.c: In function 'get_embl_format_seq': sequence_formats.c:729:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, loc_len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, loc_len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function 'add_feat': sequence_formats.c:481:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, loc_len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] 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 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 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 vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j3 --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 spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin all cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all make[2]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/spin' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/mutlib' make[2]: warning: -j3 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 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 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/./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 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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 seq_reg_cmds.c: In function 'GetActiveSeqName': seq_reg_cmds.c:919:25: warning: zero-length gnu_printf format string [-Wformat-zero-length] vTcl_SetResult(interp, ""); ^~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 seq_sendto.c: In function 'sender_callback.part.0': seq_sendto.c:132:19: warning: '%s' directive writing up to 1023 bytes into a region of size 893 [-Wformat-overflow=] sprintf(cmd, "upvar #0 commn_[list %s] commn; " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seq_sendto.c:137:39: cursor->abspos, cursor->abspos, job); ~~~ seq_sendto.c:135:25: note: format string is defined here "{abspos %d} {job %s}}]", ^~ In file included from /usr/include/stdio.h:873, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from seq_sendto.c:1: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 135 or more bytes (assuming 1158) into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 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/./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 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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j3 --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/screen_seq' make[2]: warning: -j3 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/./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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 screen_seq.c: In function 'get_vfilenames': screen_seq.c:133:18: warning: '%s' directive writing up to 4096 bytes into a region of size between 1 and 4097 [-Wformat-overflow=] sprintf(tmp, "%s%s", base_name, file_name); ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:873, from screen_seq.c:16: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 1 and 8193 bytes into a destination of size 4097 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 seqed_write.o -c seqed_write.c screen_seq.c: In function 'get_vfilenames_old': screen_seq.c:180:24: warning: '%s' directive writing up to 4096 bytes into a region of size between 1 and 4097 [-Wformat-overflow=] sprintf(file_name, "%s%s", base_name, file_name); ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:873, from screen_seq.c:16: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 1 and 8193 bytes into a destination of size 4097 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j3 --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/qclip' make[2]: warning: -j3 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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 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] fgets(line, 1024, fp); ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "##Number %d\n", &data->n_data_obj); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 1024, fp); ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "##Number %d\n", &data->n_graph_obj); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 1024, fp); ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function 'init_emboss_stick_create': emboss_input_funcs.c:658:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(dummy1, 100, fp); ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(dummy1, 100, fp); ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(dummy1, 100, fp); ^~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:316:20: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(tmp, "%10d", i*10); ^ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence_pair_display.c:344:20: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(tmp, "%10d", i*10); ^ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 compare_spans.o -c compare_spans.c make[2]: Leaving directory '/build/staden-2.0.0+b11/qclip' cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all make[2]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j3 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 -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/./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/./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 sip_hash.o -c sip_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 polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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 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/./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 make[2]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j3 --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: -j3 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/./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 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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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/./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 make[2]: Leaving directory '/build/staden-2.0.0+b11/stops' cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights 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/./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 make[2]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[2]: warning: -j3 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/./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_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/./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/./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/./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 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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/make_weights' cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j3 --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: -j3 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 -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/./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 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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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/./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 make[2]: Leaving directory '/build/staden-2.0.0+b11/find_renz' cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j3 --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: -j3 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/./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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 trna_search.o -c trna_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 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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 tg_sequence.o -c tg_sequence.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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_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/./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 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/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc 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 tg_track.o -c tg_track.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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/mutlib' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j3 --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/gap4' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/tracediff' make[2]: warning: -j3 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 tg_bin.o -c tg_bin.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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 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 actf.c: In function 'actf_lock': actf.c:246:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, db_path, strlen(db_path)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-2.0.0+b11/tracediff' cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j3 --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: -j3 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/./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 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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -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/./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/./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 /usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) 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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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 tk-io-reg.c: In function 'tk_contig_register_cmd': tk-io-reg.c:1031:15: warning: '%s' directive writing up to 1023 bytes into a region of size between 904 and 964 [-Wformat-overflow=] sprintf(buf, "{id %d} {seq %d} {pos %d} {abspos %d} {refs %d} " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tk-io-reg.c:1039:3: job); ~~~ tk-io-reg.c:1032:22: note: format string is defined here "{sent_by %d} {job %s}", ^~ In file included from /usr/include/stdio.h:873, from tk-io-reg.c:1: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 62 and 1145 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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/./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/./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/./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/./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/./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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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/./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/./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 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/./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/./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/./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/./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/./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/./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 contig_selector.o -c contig_selector.c tk-io-reg.c: In function 'tk_contig_register_cmd': tk-io-reg.c:965:15: warning: '%s' directive writing up to 1023 bytes into a region of size between 895 and 964 [-Wformat-overflow=] sprintf(buf, "{id %d} {seq %"PRIrec"} {pos %d} {abspos %d} {refs %d} " ^~~~~~~~~~~~~~~~ tk-io-reg.c:973:3: job); ~~~ tk-io-reg.c:966:22: note: format string is defined here "{sent_by %d} {job %s}", ^~ In file included from /usr/include/stdio.h:873, from tk-io-reg.c:1: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 62 and 1154 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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 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/./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/./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 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/./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/./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 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 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 consensus.o -c consensus.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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_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/./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/./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 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 template_display.o -c template_display.c gap_range.c: In function 'gap_range_x': gap_range.c:310:37: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 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/./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 template_display.c: In function 'configure_template': template_display.c:374:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); ^ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 template_display.c: In function 'template_callback': template_display.c:2354:36: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, ^~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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/./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 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 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 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/./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/./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/./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 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 contig_selector.o -c contig_selector.c readpair.c: In function 'readpair_obj_func': readpair.c:175:43: warning: '%s' directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] sprintf(cmd, "CreateTemplateDisplay %d {%s}", ^~ *handle, c_list); ~~~~~~ In file included from /usr/include/stdio.h:873, from readpair.c:18: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 27 and 1060 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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/./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/./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/./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 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 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 oligo_sel.c: In function 'primer_top.isra.2': oligo_sel.c:276:29: warning: '%s' directive writing up to 256 bytes into a region of size between 58 and 98 [-Wformat-overflow=] sprintf(tmpbuf, "%s %s %s.%d %s %d %c", ^~ tempname, gelname, dbname, *temnum, oligo, oligostart, ~~~~~~ In file included from /usr/include/stdio.h:873, from oligo_sel.c:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 306) into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 alter_rel.o -c alter_rel.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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/./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 find_oligo.c: In function 'StringMatch': find_oligo.c:957:19: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] sprintf(name1, "%"PRIrec"", ABS(c1[j])); ^~~ find_oligo.c:957:20: note: format string is defined here sprintf(name1, "%"PRIrec"", ABS(c1[j])); find_oligo.c:957:19: note: directive argument in the range [0, 9223372036854775807] sprintf(name1, "%"PRIrec"", ABS(c1[j])); ^~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 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/./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/./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/./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 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 gap_canvas_box.o -c gap_canvas_box.c copy_db.c: In function 'copy_read_name': copy_db.c:118:18: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] sprintf(num, "#%d", iter++); ^~ copy_db.c:118:16: note: directive argument in the range [1, 2147483646] sprintf(num, "#%d", iter++); ^~~~~ In file included from /usr/include/stdio.h:873, from copy_db.c:1: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 notes.o -c notes.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=] sprintf(buf, "%s (%ld)", buf2, (long)t); ^~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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/./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/./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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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 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/./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 consistency_display.c: In function 'consistency_callback': consistency_display.c:883:36: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, ^~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 readpair_coverage.o -c readpair_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 strand_coverage.o -c strand_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/./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/./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 find_fragments.o -c find_fragments.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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 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/./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 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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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 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=] sprintf(buf, "%s xview moveto %g;%s icursor %d\n", ^~~~~~~~~~~~~~ tman_display.c:279:18: note: assuming directive output of 12 bytes sprintf(buf, "%s xview moveto %g;%s icursor %d\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c: In function 'manageTrace': tman_display.c:250:21: warning: ' left_cutoff ' directive writing 13 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(buf, "%s left_cutoff %d", dc->path, leftCutOff); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 1048 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:253:21: warning: ' right_cutoff ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(buf, "%s right_cutoff %d", dc->path, leftCutOff + cutLength); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 1049 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 editor_oligo.o -c editor_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 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/./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 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/./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/./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/./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 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/./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/./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/./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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -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 tagEditor.o -c tagEditor.c /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/tg_index_common.c:105: warning: the use of `tmpnam' is dangerous, better use `mkstemp' 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -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 searchUtils.o -c searchUtils.c /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-2.0.0+b11/gap5' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 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=] sprintf(buf, "%s xview moveto %g;%s icursor %d\n", ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes sprintf(buf, "%s xview moveto %g;%s icursor %d\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c: In function 'manageTrace': tman_display.c:252:21: warning: ' left_cutoff ' directive writing 13 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(buf, "%s left_cutoff %d", dc->path, leftCutOff); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 1048 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:255:21: warning: ' right_cutoff ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(buf, "%s right_cutoff %d", dc->path, leftCutOff + cutLength); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, 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: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 1049 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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:86:2: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%c", &ans); ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz 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/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/gap4' cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all make[2]: Entering directory '/build/staden-2.0.0+b11/haplo' make[2]: warning: -j3 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/prefinish' make[2]: warning: -j3 forced in submake: resetting jobserver mode. cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all make[2]: Entering directory '/build/staden-2.0.0+b11/copy_reads' make[2]: warning: -j3 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/./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/./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_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/./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/./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/./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/./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 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=] sprintf(comment, "%s %s", tag_text, io_name(io)); ^~ In file included from /usr/include/stdio.h:873, from copy_reads.c:4: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 copy_reads.c: In function 'copy_reads': copy_reads.c:409:27: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] sprintf(comment, "%s %s", tag_text, io_name(io_to)); ^~ In file included from /usr/include/stdio.h:873, from copy_reads.c:4: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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/./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 -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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j3 --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/convert' make[2]: warning: -j3 forced in submake: resetting jobserver mode. 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/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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/./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 main.c: In function 'get_db': main.c:87:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(name, sizeof(IOString), stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(version, sizeof(IOString), stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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_reverse.o -c finish_reverse.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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/./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_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/./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/./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 gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 read_size_dist.o -c read_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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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_conf_dist.o -c read_conf_dist.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/./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/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 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/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -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/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-2.0.0+b11/convert' /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) 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/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) 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 -j3 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/arm-linux-gnueabihf/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 -j3 --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 -j3 --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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install make[4]: Entering directory '/build/staden-2.0.0+b11/Misc' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/trev' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/primer3' make[4]: warning: -j3 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/arm-linux-gnueabihf/staden install trev /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3' make[4]: Leaving directory '/build/staden-2.0.0+b11/Misc' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install cp /build/staden-2.0.0+b11/./trev/trev.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install make[4]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./trev/trevrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/trev' /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' cp /build/staden-2.0.0+b11/lib/libprimer3.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' 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 cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins install /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]: Entering directory '/build/staden-2.0.0+b11/hetins' make[4]: warning: -j3 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss 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 cp hetins /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/hetins' cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j3 --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/scripts' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules 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/pregap4/templates mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes 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 /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' 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 /build/staden-2.0.0+b11/./scripts/assemble4 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts 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 cp /build/staden-2.0.0+b11/./scripts/fasta-split /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' cp /build/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j3 --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/./scripts/splitseq_da /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/staden-2.0.0+b11/data' make[4]: warning: -j3 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' /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' cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/staden-2.0.0+b11/./data/alus/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus make[4]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libtk_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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 mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-2.0.0+b11/./pregap4/pregap4rc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/pregap4' cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install make[4]: Entering directory '/build/staden-2.0.0+b11/text_utils' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/text_utils' cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi install make[4]: Entering directory '/build/staden-2.0.0+b11/abi' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp getABISampleName getABIcomment getABIdate getABIfield /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/abi' cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j3 --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/./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 make[4]: Entering directory '/build/staden-2.0.0+b11/alf' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g install make[4]: Leaving directory '/build/staden-2.0.0+b11/alf' make[4]: Entering directory '/build/staden-2.0.0+b11/g' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba install make[4]: Entering directory '/build/staden-2.0.0+b11/eba' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp eba /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libg.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/eba' make[4]: Leaving directory '/build/staden-2.0.0+b11/g' 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 cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j3 --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 make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp init_exp /build/staden-2.0.0+b11/debian/tmp/usr/bin cp get_scf_field /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/init_exp' make[4]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' cp /build/staden-2.0.0+b11/./data/gcodes/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libseq_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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' 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 cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j3 --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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin install make[4]: Entering directory '/build/staden-2.0.0+b11/mutlib' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./data/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/lib/libmutlib.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden install spin /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./data/renzyme_bairoch /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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 /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 vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install cp /build/staden-2.0.0+b11/./data/m13mp18_primers /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./data/vector_primer /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./data/pam250 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp vector_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/data' make[4]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install make[4]: Entering directory '/build/staden-2.0.0+b11/tracediff' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install make[4]: Entering directory '/build/staden-2.0.0+b11/screen_seq' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp tracediff /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/tracediff' cp screen_seq /build/staden-2.0.0+b11/debian/tmp/usr/bin cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip install make[4]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' cp /build/staden-2.0.0+b11/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Entering directory '/build/staden-2.0.0+b11/qclip' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j3 --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]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp polyA_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops install make[4]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: Entering directory '/build/staden-2.0.0+b11/stops' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j3 --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 /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 make[4]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin cp make_weights /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/stops' make[4]: Leaving directory '/build/staden-2.0.0+b11/spin' make[4]: Leaving directory '/build/staden-2.0.0+b11/make_weights' cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j3 --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 -j3 --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 -j3 --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/mutscan' make[4]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/find_renz' make[4]: Leaving directory '/build/staden-2.0.0+b11/mutscan' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install make[4]: Entering directory '/build/staden-2.0.0+b11/gap4' make[4]: warning: -j3 forced in submake: resetting jobserver mode. install gap5 /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 cp copy_db /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 cp /build/staden-2.0.0+b11/./gap5/../gap4/acd2tag.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 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/arm-linux-gnueabihf/staden cp tg_index.bin /build/staden-2.0.0+b11/debian/tmp/usr/bin install tg_index /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libgap.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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/./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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j3 --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 -j3 --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/prefinish' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/copy_reads' make[4]: Entering directory '/build/staden-2.0.0+b11/haplo' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: warning: -j3 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish mkdir /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/./haplo/*.tcl /build/staden-2.0.0+b11/./haplo/tclIndex /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/copy_reads install copy_reads /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libhaplo.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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 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/lib/libcopy_reads.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/haplo' cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert install cp /build/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-2.0.0+b11/convert' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' 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/arm-linux-gnueabihf/staden cp staden_convert /build/staden-2.0.0+b11/debian/tmp/usr/bin install prefinish /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/convert' 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/arm-linux-gnueabihf/* /build/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: 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 dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libfreetype.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libXss.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libXext.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/bin/copy_db debian/staden/usr/lib/staden/bin/make_weights debian/staden/usr/lib/staden/bin/getABIcomment debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/bin/staden_convert debian/staden/usr/lib/staden/bin/polyA_clip debian/staden/usr/lib/staden/bin/vector_clip debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/bin/getABIfield debian/staden/usr/lib/staden/bin/stops debian/staden/usr/lib/staden/bin/tracediff debian/staden/usr/lib/staden/bin/init_exp debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/getABISampleName debian/staden/usr/lib/staden/bin/eba debian/staden/usr/lib/staden/bin/hetins debian/staden/usr/lib/staden/bin/find_renz debian/staden/usr/lib/staden/bin/get_scf_field debian/staden/usr/lib/staden/bin/qclip debian/staden/usr/lib/staden/bin/tg_index.bin debian/staden/usr/lib/staden/bin/screen_seq were not linked against libcurl-gnutls.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/bin/copy_db debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libdl.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libXft.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/staden/usr/lib/staden/libprefinish.so debian/staden/usr/lib/staden/libcopy_reads.so debian/staden/usr/lib/staden/libspin.so debian/staden/usr/lib/staden/libgap.so debian/staden/usr/lib/staden/libgap5.so debian/staden/usr/lib/staden/bin/mutscan debian/staden/usr/lib/staden/libhaplo.so debian/staden/usr/lib/staden/libtk_utils.so debian/staden/usr/lib/staden/libmutlib.so debian/staden/usr/lib/staden/bin/tg_index.bin were not linked against libfontconfig.so.1 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4_armhf.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-4_all.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../staden_2.0.0+b11-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14608 and its subdirectories I: Current time: Mon Oct 26 05:12:37 -12 2020 I: pbuilder-time-stamp: 1603732357