I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 28 15:20:06 -12 2021 I: pbuilder-time-stamp: 1627528806 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: 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 '/tmp/dpkg-verify-sig.OBaXncsE/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/2774/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,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='f99f7413b82942588471e78044dc5054' 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='2774' 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.UKxSQr9UQ4/pbuilderrc_thjp --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UKxSQr9UQ4/b1 --logfile b1/build.log staden_2.0.0+b11-4.dsc' SUDO_GID='116' SUDO_UID='112' 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 cbxi4b 5.10.0-8-armmp #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 24 21:29 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/2774/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 ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev (>= 1.14.6); however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on itcl3-dev; however: Package itcl3-dev is not installed. pbuilder-satisfydepends-dummy depends on itk3-dev; however: Package itk3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on tcl-dev; however: Package tcl-dev is not installed. pbuilder-satisfydepends-dummy depends on tk-dev; however: Package tk-dev is not installed. pbuilder-satisfydepends-dummy depends on tklib; however: Package tklib is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on iwidgets4; however: Package iwidgets4 is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} itcl3{a} itcl3-dev{a} itk3{a} itk3-dev{a} iwidgets4{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libfreetype6-dev{a} libglib2.0-0{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libssh2-1{a} libstaden-read-dev{a} libstaden-read14{a} libsub-override-perl{a} libtcl8.6{a} libtk8.6{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft-dev{a} libxft2{a} libxml2{a} libxrender-dev{a} libxrender1{a} libxss-dev{a} libxss1{a} m4{a} man-db{a} pkg-config{a} 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 cool-retro-term curl deepin-terminal eterm gnome-terminal kitty konsole libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules lxterminal lynx mate-terminal mlterm mlterm-tiny pterm publicsuffix qterminal rxvt-unicode sakura shared-mime-info stterm tcllib terminator terminology termit wget xdg-user-dirs xfce4-terminal xiterm+thai xterm 0 packages upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 37.7 MB of archives. After unpacking 118 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf libtcl8.6 armhf 8.6.11+dfsg-1 [913 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf libpng16-16 armhf 1.6.37-3 [277 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [357 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf ucf all 3.0043 [74.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf fonts-dejavu-core all 2.37-2 [1069 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf fontconfig-config all 2.13.1-4.2 [281 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf libfontconfig1 armhf 2.13.1-4.2 [329 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.1-1 [310 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.1-1 [712 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libxft2 armhf 2.3.2-2 [50.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf x11-common all 1:7.7+22 [252 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libtk8.6 armhf 8.6.11-2 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf itcl3 armhf 3.4.3-3.1 [45.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf itk3 armhf 3.4.2-3.1 [26.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf tcl8.6 armhf 8.6.11+dfsg-1 [124 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf tcl8.6-dev armhf 8.6.11+dfsg-1 [938 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf tcl armhf 8.6.11+1 [5788 B] Get: 60 http://deb.debian.org/debian bullseye/main armhf tcl-dev armhf 8.6.11+1 [8352 B] Get: 61 http://deb.debian.org/debian bullseye/main armhf itcl3-dev armhf 3.4.3-3.1 [15.5 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf x11proto-dev all 2020.1-1 [594 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf x11proto-core-dev all 2020.1-1 [3404 B] Get: 65 http://deb.debian.org/debian bullseye/main armhf libxau-dev armhf 1:1.0.9-1 [22.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.7 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf xtrans-dev all 1.4.0-1 [98.7 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B] Get: 69 http://deb.debian.org/debian bullseye/main armhf libxcb1-dev armhf 1.14-3 [175 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libx11-dev armhf 2:1.7.1-1 [787 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf x11proto-xext-dev all 2020.1-1 [3404 B] Get: 72 http://deb.debian.org/debian bullseye/main armhf libxext-dev armhf 2:1.3.3-1.1 [103 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf x11proto-scrnsaver-dev all 2020.1-1 [3412 B] Get: 74 http://deb.debian.org/debian bullseye/main armhf libxss-dev armhf 1:1.2.3-1 [23.1 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libexpat1-dev armhf 2.2.10-2 [123 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libbrotli-dev armhf 1.0.9-2+b2 [270 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libpng-dev armhf 1.6.37-3 [282 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libfreetype-dev armhf 2.10.4+dfsg-1 [516 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libfreetype6-dev armhf 2.10.4+dfsg-1 [82.4 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf uuid-dev armhf 2.36.1-7 [97.9 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libfontconfig-dev armhf 2.13.1-4.2 [353 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libfontconfig1-dev armhf 2.13.1-4.2 [238 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libxrender-dev armhf 1:0.9.10-1 [37.8 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libxft-dev armhf 2.3.2-2 [62.3 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf tk8.6 armhf 8.6.11-2 [72.2 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf tk8.6-dev armhf 8.6.11-2 [718 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf tk armhf 8.6.11+1 [5828 B] Get: 90 http://deb.debian.org/debian bullseye/main armhf tk-dev armhf 8.6.11+1 [5652 B] Get: 91 http://deb.debian.org/debian bullseye/main armhf itk3-dev armhf 3.4.2-3.1 [5504 B] Get: 92 http://deb.debian.org/debian bullseye/main armhf iwidgets4 all 4.1.1-2.1 [195 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf libbz2-dev armhf 1.0.8-4 [29.2 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 95 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 98 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 99 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 100 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 101 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 102 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+b1 [402 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf libhtscodecs2 armhf 0.5-3 [48.5 kB] Get: 104 http://deb.debian.org/debian bullseye/main armhf libhtscodecs-dev armhf 0.5-3 [2518 kB] Get: 105 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB] Get: 106 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 107 http://deb.debian.org/debian bullseye/main armhf libncurses-dev armhf 6.2+20201114-2 [308 kB] Get: 108 http://deb.debian.org/debian bullseye/main armhf libncurses5-dev armhf 6.2+20201114-2 [936 B] Get: 109 http://deb.debian.org/debian bullseye/main armhf libstaden-read14 armhf 1.14.13-4 [235 kB] Get: 110 http://deb.debian.org/debian bullseye/main armhf libstaden-read-dev armhf 1.14.13-4 [313 kB] Get: 111 http://deb.debian.org/debian bullseye/main armhf tklib all 0.7+20210111-1 [1280 kB] Fetched 37.7 MB in 4s (9671 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../001-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../003-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libtcl8.6:armhf. Preparing to unpack .../005-libtcl8.6_8.6.11+dfsg-1_armhf.deb ... Unpacking libtcl8.6:armhf (8.6.11+dfsg-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../006-libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../007-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../008-libpng16-16_1.6.37-3_armhf.deb ... Unpacking libpng16-16:armhf (1.6.37-3) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../009-libfreetype6_2.10.4+dfsg-1_armhf.deb ... Unpacking libfreetype6:armhf (2.10.4+dfsg-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../010-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../012-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../013-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../014-libfontconfig1_2.13.1-4.2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-4.2) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../015-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libmd0:armhf. Preparing to unpack .../016-libmd0_1.0.3-3_armhf.deb ... Unpacking libmd0:armhf (1.0.3-3) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../017-libbsd0_0.11.3-1_armhf.deb ... Unpacking libbsd0:armhf (0.11.3-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../018-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 .../019-libxcb1_1.14-3_armhf.deb ... Unpacking libxcb1:armhf (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../020-libx11-data_2%3a1.7.1-1_all.deb ... Unpacking libx11-data (2:1.7.1-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../021-libx11-6_2%3a1.7.1-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.7.1-1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../022-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 .../023-libxft2_2.3.2-2_armhf.deb ... Unpacking libxft2:armhf (2.3.2-2) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../024-libxext6_2%3a1.3.3-1.1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1.1) ... Selecting previously unselected package x11-common. Preparing to unpack .../025-x11-common_1%3a7.7+22_all.deb ... Unpacking x11-common (1:7.7+22) ... Selecting previously unselected package libxss1:armhf. Preparing to unpack .../026-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 .../027-libtk8.6_8.6.11-2_armhf.deb ... Unpacking libtk8.6:armhf (8.6.11-2) ... Selecting previously unselected package itcl3:armhf. Preparing to unpack .../028-itcl3_3.4.3-3.1_armhf.deb ... Unpacking itcl3:armhf (3.4.3-3.1) ... Selecting previously unselected package itk3:armhf. Preparing to unpack .../029-itk3_3.4.2-3.1_armhf.deb ... Unpacking itk3:armhf (3.4.2-3.1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../030-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../031-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../032-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../033-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../034-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../035-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../036-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../037-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../038-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../039-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../040-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../041-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../042-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../043-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../044-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../045-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../046-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../047-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../048-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../049-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../050-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... 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+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../055-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../056-tcl8.6_8.6.11+dfsg-1_armhf.deb ... Unpacking tcl8.6 (8.6.11+dfsg-1) ... Selecting previously unselected package tcl8.6-dev:armhf. Preparing to unpack .../057-tcl8.6-dev_8.6.11+dfsg-1_armhf.deb ... Unpacking tcl8.6-dev:armhf (8.6.11+dfsg-1) ... Selecting previously unselected package tcl. Preparing to unpack .../058-tcl_8.6.11+1_armhf.deb ... Unpacking tcl (8.6.11+1) ... Selecting previously unselected package tcl-dev:armhf. Preparing to unpack .../059-tcl-dev_8.6.11+1_armhf.deb ... Unpacking tcl-dev:armhf (8.6.11+1) ... Selecting previously unselected package itcl3-dev:armhf. Preparing to unpack .../060-itcl3-dev_3.4.3-3.1_armhf.deb ... Unpacking itcl3-dev:armhf (3.4.3-3.1) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../061-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../062-x11proto-dev_2020.1-1_all.deb ... Unpacking x11proto-dev (2020.1-1) ... Selecting previously unselected package x11proto-core-dev. Preparing to unpack .../063-x11proto-core-dev_2020.1-1_all.deb ... Unpacking x11proto-core-dev (2020.1-1) ... Selecting previously unselected package libxau-dev:armhf. Preparing to unpack .../064-libxau-dev_1%3a1.0.9-1_armhf.deb ... Unpacking libxau-dev:armhf (1:1.0.9-1) ... 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_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... 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_1.14-3_armhf.deb ... Unpacking libxcb1-dev:armhf (1.14-3) ... Selecting previously unselected package libx11-dev:armhf. Preparing to unpack .../069-libx11-dev_2%3a1.7.1-1_armhf.deb ... Unpacking libx11-dev:armhf (2:1.7.1-1) ... Selecting previously unselected package x11proto-xext-dev. Preparing to unpack .../070-x11proto-xext-dev_2020.1-1_all.deb ... Unpacking x11proto-xext-dev (2020.1-1) ... Selecting previously unselected package libxext-dev:armhf. Preparing to unpack .../071-libxext-dev_2%3a1.3.3-1.1_armhf.deb ... Unpacking libxext-dev:armhf (2:1.3.3-1.1) ... Selecting previously unselected package x11proto-scrnsaver-dev. Preparing to unpack .../072-x11proto-scrnsaver-dev_2020.1-1_all.deb ... Unpacking x11proto-scrnsaver-dev (2020.1-1) ... Selecting previously unselected package libxss-dev:armhf. Preparing to unpack .../073-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 .../074-libexpat1-dev_2.2.10-2_armhf.deb ... Unpacking libexpat1-dev:armhf (2.2.10-2) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../075-libbrotli-dev_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli-dev:armhf (1.0.9-2+b2) ... Selecting previously unselected package libpng-dev:armhf. Preparing to unpack .../076-libpng-dev_1.6.37-3_armhf.deb ... Unpacking libpng-dev:armhf (1.6.37-3) ... Selecting previously unselected package libfreetype-dev:armhf. Preparing to unpack .../077-libfreetype-dev_2.10.4+dfsg-1_armhf.deb ... Unpacking libfreetype-dev:armhf (2.10.4+dfsg-1) ... Selecting previously unselected package libfreetype6-dev:armhf. Preparing to unpack .../078-libfreetype6-dev_2.10.4+dfsg-1_armhf.deb ... Unpacking libfreetype6-dev:armhf (2.10.4+dfsg-1) ... Selecting previously unselected package uuid-dev:armhf. Preparing to unpack .../079-uuid-dev_2.36.1-7_armhf.deb ... Unpacking uuid-dev:armhf (2.36.1-7) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../080-libglib2.0-0_2.66.8-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.66.8-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../081-pkg-config_0.29.2-1_armhf.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package libfontconfig-dev:armhf. Preparing to unpack .../082-libfontconfig-dev_2.13.1-4.2_armhf.deb ... Unpacking libfontconfig-dev:armhf (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1-dev:armhf. Preparing to unpack .../083-libfontconfig1-dev_2.13.1-4.2_armhf.deb ... Unpacking libfontconfig1-dev:armhf (2.13.1-4.2) ... Selecting previously unselected package libxrender-dev:armhf. Preparing to unpack .../084-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 .../085-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 .../086-tk8.6_8.6.11-2_armhf.deb ... Unpacking tk8.6 (8.6.11-2) ... Selecting previously unselected package tk8.6-dev:armhf. Preparing to unpack .../087-tk8.6-dev_8.6.11-2_armhf.deb ... Unpacking tk8.6-dev:armhf (8.6.11-2) ... Selecting previously unselected package tk. Preparing to unpack .../088-tk_8.6.11+1_armhf.deb ... Unpacking tk (8.6.11+1) ... Selecting previously unselected package tk-dev:armhf. Preparing to unpack .../089-tk-dev_8.6.11+1_armhf.deb ... Unpacking tk-dev:armhf (8.6.11+1) ... Selecting previously unselected package itk3-dev:armhf. Preparing to unpack .../090-itk3-dev_3.4.2-3.1_armhf.deb ... Unpacking itk3-dev:armhf (3.4.2-3.1) ... Selecting previously unselected package iwidgets4. Preparing to unpack .../091-iwidgets4_4.1.1-2.1_all.deb ... Unpacking iwidgets4 (4.1.1-2.1) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../092-libbz2-dev_1.0.8-4_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-4) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../093-libsasl2-modules-db_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../094-libsasl2-2_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../095-libldap-2.4-2_2.4.57+dfsg-3_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../096-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../097-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../098-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../099-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../100-libcurl3-gnutls_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../101-libcurl4-gnutls-dev_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../102-libhtscodecs2_0.5-3_armhf.deb ... Unpacking libhtscodecs2:armhf (0.5-3) ... Selecting previously unselected package libhtscodecs-dev:armhf. Preparing to unpack .../103-libhtscodecs-dev_0.5-3_armhf.deb ... Unpacking libhtscodecs-dev:armhf (0.5-3) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../104-liblzma-dev_5.2.5-2_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.5-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../105-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../106-libncurses-dev_6.2+20201114-2_armhf.deb ... Unpacking libncurses-dev:armhf (6.2+20201114-2) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../107-libncurses5-dev_6.2+20201114-2_armhf.deb ... Unpacking libncurses5-dev:armhf (6.2+20201114-2) ... Selecting previously unselected package libstaden-read14:armhf. Preparing to unpack .../108-libstaden-read14_1.14.13-4_armhf.deb ... Unpacking libstaden-read14:armhf (1.14.13-4) ... Selecting previously unselected package libstaden-read-dev. Preparing to unpack .../109-libstaden-read-dev_1.14.13-4_armhf.deb ... Unpacking libstaden-read-dev (1.14.13-4) ... Selecting previously unselected package tklib. Preparing to unpack .../110-tklib_0.7+20210111-1_all.deb ... Unpacking tklib (0.7+20210111-1) ... Setting up libhtscodecs2:armhf (0.5-3) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libpthread-stubs0-dev:armhf (0.4-1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Setting up libhtscodecs-dev:armhf (0.5-3) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libexpat1-dev:armhf (2.2.10-2) ... Setting up libx11-data (2:1.7.1-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up uuid-dev:armhf (2.36.1-7) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up libpng16-16:armhf (1.6.37-3) ... Setting up libtcl8.6:armhf (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:armhf (5.2.5-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up libmd0:armhf (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libbsd0:armhf (0.11.3-1) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libbrotli-dev:armhf (1.0.9-2+b2) ... Setting up libbz2-dev:armhf (1.0.8-4) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up tcl8.6 (8.6.11+dfsg-1) ... Setting up libncurses-dev:armhf (6.2+20201114-2) ... Setting up libxcb1:armhf (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libxau-dev:armhf (1:1.0.9-1) ... Setting up libtool (2.4.6-15) ... Setting up tcl8.6-dev:armhf (8.6.11+dfsg-1) ... Setting up libpng-dev:armhf (1.6.37-3) ... Setting up itcl3:armhf (3.4.3-3.1) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxdmcp-dev:armhf (1:1.1.2-3) ... Setting up libfreetype6:armhf (2.10.4+dfsg-1) ... Setting up x11proto-core-dev (2020.1-1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up tcl (8.6.11+1) ... Setting up libncurses5-dev:armhf (6.2+20201114-2) ... Setting up libx11-6:armhf (2:1.7.1-1) ... Setting up libstaden-read14:armhf (1.14.13-4) ... Setting up x11proto-scrnsaver-dev (2020.1-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up itcl3-dev:armhf (3.4.3-3.1) ... Setting up libxcb1-dev:armhf (1.14-3) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libstaden-read-dev (1.14.13-4) ... Setting up libx11-dev:armhf (2:1.7.1-1) ... Setting up libxext6:armhf (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libfreetype-dev:armhf (2.10.4+dfsg-1) ... Setting up dh-autoreconf (20) ... Setting up tcl-dev:armhf (8.6.11+1) ... Setting up libxext-dev:armhf (2:1.3.3-1.1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libfontconfig1:armhf (2.13.1-4.2) ... Setting up libxrender-dev:armhf (1:0.9.10-1) ... Setting up libxft2:armhf (2.3.2-2) ... Setting up libtk8.6:armhf (8.6.11-2) ... Setting up debhelper (13.3.4) ... Setting up libxss-dev:armhf (1:1.2.3-1) ... Setting up libfreetype6-dev:armhf (2.10.4+dfsg-1) ... Setting up itk3:armhf (3.4.2-3.1) ... Setting up iwidgets4 (4.1.1-2.1) ... Setting up tk8.6 (8.6.11-2) ... Setting up libfontconfig-dev:armhf (2.13.1-4.2) ... Setting up tk (8.6.11+1) ... Setting up libxft-dev:armhf (2.3.2-2) ... Setting up libfontconfig1-dev:armhf (2.13.1-4.2) ... Setting up tklib (0.7+20210111-1) ... Setting up tk8.6-dev:armhf (8.6.11-2) ... Setting up itk3-dev:armhf (3.4.2-3.1) ... Setting up tk-dev:armhf (8.6.11+1) ... Processing triggers for libc-bin (2.31-13) ... 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 (1.25.3-1.1). 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden_2.0.0+b11-4_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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-option-checking --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 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... 7.74.0 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... no checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking if 64bit support is requested... no checking if 64bit Sparc VIS support is requested... no checking if compiler supports visibility "hidden"... yes checking if rpath support is requested... yes checking system version... Linux-5.10.0-8-armmp 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/tklib0.7) 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 ---------------------------------------------------------------------- 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/tklib0.7 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 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 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 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/trev' 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. make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/trev' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c cd 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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c Nothing to build for Pregap4. make[2]: Leaving directory '/build/staden-2.0.0+b11/pregap4' gcc -g -O2 -fdebug-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 -fdebug-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 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' 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. gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 /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' Nothing to build for scripts. make[2]: Leaving directory '/build/staden-2.0.0+b11/scripts' gcc -g -O2 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 In file included from /usr/include/string.h:495, from strings.c:4: In function 'strncpy', inlined from 'c2fstr' at strings.c:31:5: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from strings.c:1: strings.c: In function 'c2fstr': strings.c:30:18: note: length computed here 30 | i = min((int)strlen(c),max_f); | ^~~~~~~~~ misc.h:87:23: note: in definition of macro 'min' 87 | #define min(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 416 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:416:23: note: directive argument in the range [1, 53687092] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o misc.o -c misc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 234 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:234:23: note: directive argument in the range [1, 2147483647] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -fdebug-prefix-map=/build/staden-2.0.0+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] 347 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 363 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function 'readIndexEntry': alfsplit.c:129:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | fread (ent->label,40,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:135:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 135 | fread (junk,70,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function 'main': alfsplit.c:312:22: warning: '%s' directive writing up to 2559 bytes into a region of size 25 [-Wformat-overflow=] 312 | sprintf (fname,"%sALF",name[i]) ; | ^~ In file included from /usr/include/stdio.h:867, from alfsplit.c:30: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 2563 bytes into a destination of size 25 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -shared -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceIO.o -c tkTraceIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceDisp.o -c tkTraceDisp.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/g' 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 -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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/eba' 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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./get_scf_field -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o 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 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=] 746 | sprintf(number, "%d", cind); | ^ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' capture.c: In function 'tcl_capture': capture.c:33:7: warning: implicit declaration of function 'mkostemp'; did you mean 'mkstemp'? [-Wimplicit-function-declaration] 33 | fd = mkostemp(NULL, 0666); | ^~~~~~~~ | mkstemp capture.c:54:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | read(fd, buf, statbuf.st_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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=] 1049 | sprintf(colour, "#%02x%02x%02x", r, g, b); | ^ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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] 729 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 738 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function 'add_feat': sequence_formats.c:481:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 481 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 510 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin all cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -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 make[2]: Entering directory '/build/staden-2.0.0+b11/mutlib' 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/vector_clip' make[2]: warning: -j3 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 g++ -g -O2 -fdebug-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] 919 | vTcl_SetResult(interp, ""); | ^~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 g++ -g -O2 -fdebug-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 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 g++ -g -O2 -fdebug-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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./screen_seq -I/build/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 emboss_input_funcs.c: In function 'read_emboss_data_file': emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 402 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 444 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:6: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 477 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function 'init_emboss_stick_create': emboss_input_funcs.c:658:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 658 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 659 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ 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=] 316 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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=] 344 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 g++ -g -O2 -fdebug-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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c g++ -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 -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 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. gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c gcc -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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./stops -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c gcc -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 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 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -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 g++ -g -O2 -fdebug-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 make[2]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[2]: warning: -j3 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c gcc -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 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c g++ -g -O2 -fdebug-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 -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 make[2]: Leaving directory '/build/staden-2.0.0+b11/spin' g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-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 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 make[2]: Entering directory '/build/staden-2.0.0+b11/gap4' make[2]: warning: -j3 forced in submake: resetting jobserver mode. 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/tracediff' make[2]: warning: -j3 forced in submake: resetting jobserver mode. g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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 actf.c: In function 'actf_lock': actf.c:246:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 246 | write(fd, db_path, strlen(db_path)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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) gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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. gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 g++ -g -O2 -fdebug-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 -fdebug-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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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 /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) gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/mutscan' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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] 310 | if (!HashTableSearch(lib_recs, (char *)r->library_rec, | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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] 374 | HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, | ^~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", | ^~ 176 | *handle, c_list); | ~~~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ find_oligo.c:957:20: note: format string is defined here 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); find_oligo.c:957:19: note: directive argument in the range [0, 9223372036854775807] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 118 | sprintf(num, "#%d", iter++); | ^~ copy_db.c:118:16: note: directive argument in the range [1, 2147483646] 118 | sprintf(num, "#%d", iter++); | ^~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 notes.c: In function 'time_t2str': notes.c:829:21: warning: ' (' directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 829 | sprintf(buf, "%s (%ld)", buf2, (long)t); | ^~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 883 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, | ^~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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=] 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:279:18: note: assuming directive output of 12 bytes 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 In file included from /usr/include/string.h:495, from caf.c:11: In function 'strncpy', inlined from 'read_data' at caf.c:1044:3: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ caf.c: In function 'read_data': caf.c:1036:16: note: length computed here 1036 | tm_len = strlen(value); | ^~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from caf.c:11: In function 'strncpy', inlined from 'read_data' at caf.c:1033:3: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ caf.c: In function 'read_data': caf.c:1027:16: note: length computed here 1027 | tr_len = strlen(value); | ^~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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: 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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -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 /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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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' 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]: 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. 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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 'create_si_struct': copy_reads.c:125:26: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 125 | sprintf(comment, "%s %s", tag_text, io_name(io)); | ^~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); | ^~ In file included from /usr/include/stdio.h:867, 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 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -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) /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) 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) make[2]: Leaving directory '/build/staden-2.0.0+b11/convert' 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 make[4]: Entering directory '/build/staden-2.0.0+b11/Misc' make[4]: 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 install 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]: 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 make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3' 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/trev.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev 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 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/eba' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/trev' 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 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp eba /build/staden-2.0.0+b11/debian/tmp/usr/bin 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]: Leaving directory '/build/staden-2.0.0+b11/eba' make[4]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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/pregap4' 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/get_scf_field' make[4]: Leaving directory '/build/staden-2.0.0+b11/init_exp' /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' 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 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 install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 make[4]: Entering directory '/build/staden-2.0.0+b11/hetins' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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 /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' mkdir /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 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 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/pregap4/templates make[4]: Leaving directory '/build/staden-2.0.0+b11/hetins' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules 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/spin_emboss/acdtcl 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/./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 cp /build/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' 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 cp /build/staden-2.0.0+b11/./scripts/staden_help /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/./pregap4/templates/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates make[4]: Leaving directory '/build/staden-2.0.0+b11/scripts' cp: cannot stat '/build/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory /build/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' make[4]: [/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 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/./pregap4/pregap4rc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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/./data/alus/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus 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/libtk_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-2.0.0+b11/./tk_utils/*.tcl /build/staden-2.0.0+b11/./tk_utils/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-2.0.0+b11/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 make[4]: Entering directory '/build/staden-2.0.0+b11/alf' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: 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 install make[4]: Entering directory '/build/staden-2.0.0+b11/g' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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/g' 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]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data 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 cp /build/staden-2.0.0+b11/./data/blast_data/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' 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 mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./data/gcodes/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes make[4]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -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. 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 cp /build/staden-2.0.0+b11/lib/libmutlib.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/mutlib' install spin /build/staden-2.0.0+b11/debian/tmp/usr/bin 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/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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 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/renzyme_bairoch /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./data/m13mp18_primers /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 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' make[4]: Leaving directory '/build/staden-2.0.0+b11/data' 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. cp /build/staden-2.0.0+b11/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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 /build/staden-2.0.0+b11/./spin/*.wts /build/staden-2.0.0+b11/./spin/niprc /build/staden-2.0.0+b11/./spin/siprc /build/staden-2.0.0+b11/./spin/spinrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp 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' make[4]: Leaving directory '/build/staden-2.0.0+b11/spin' 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 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]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/stops' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' cp polyA_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: Leaving directory '/build/staden-2.0.0+b11/stops' 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 make[4]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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 make[4]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/mutscan' make[4]: warning: -j3 forced in submake: resetting jobserver mode. cp make_weights /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/make_weights' 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 cp find_renz /build/staden-2.0.0+b11/debian/tmp/usr/bin cp mutscan /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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 /build/staden-2.0.0+b11/lib/libgap.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/./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 install gap5_cmd /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/gap5' 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/haplo' make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/copy_reads' 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/./haplo/*.tcl /build/staden-2.0.0+b11/./haplo/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo cp /build/staden-2.0.0+b11/./prefinish/*.tcl /build/staden-2.0.0+b11/./prefinish/*.itcl /build/staden-2.0.0+b11/./prefinish/*.itk /build/staden-2.0.0+b11/./prefinish/help /build/staden-2.0.0+b11/./prefinish/args.template /build/staden-2.0.0+b11/./prefinish/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish 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/./haplo/haplorc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/staden-2.0.0+b11/./copy_reads/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads make[4]: Leaving directory '/build/staden-2.0.0+b11/haplo' 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/lib/libcopy_reads.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_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: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4_armhf.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_armhf.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-4_all.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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2774 and its subdirectories I: Current time: Wed Jul 28 15:33:52 -12 2021 I: pbuilder-time-stamp: 1627529632