Mon Jun 21 20:33:59 UTC 2021 I: starting to build staden/bullseye/i386 on jenkins on '2021-06-21 20:33' Mon Jun 21 20:33:59 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/10594/console.log Mon Jun 21 20:33:59 UTC 2021 I: Downloading source for bullseye/staden=2.0.0+b11-4 --2021-06-21 20:34:00-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/staden/staden_2.0.0+b11-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2218 (2.2K) Saving to: ‘staden_2.0.0+b11-4.dsc’ 0K .. 100% 157M=0s 2021-06-21 20:34:00 (157 MB/s) - ‘staden_2.0.0+b11-4.dsc’ saved [2218/2218] Mon Jun 21 20:34:00 UTC 2021 I: staden_2.0.0+b11-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: staden Binary: staden, staden-common Architecture: any all Version: 2.0.0+b11-4 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://sourceforge.net/projects/staden/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/staden Vcs-Git: https://salsa.debian.org/med-team/staden.git Build-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 Package-List: staden deb science optional arch=any staden-common deb science optional arch=all Checksums-Sha1: a51f0a004961511734a05fd54d8b2b1b0cfd6e32 4754651 staden_2.0.0+b11.orig.tar.gz aecb4718ce533a6aae2ed37550b16b8e8f1a27d6 16320 staden_2.0.0+b11-4.debian.tar.xz Checksums-Sha256: cd7ee17626c25bc845ebd3f6311b5a538815fb73a0dfef2393001bf579ac9649 4754651 staden_2.0.0+b11.orig.tar.gz b35af6e736d8eb0421660c9e132869f352d7a5ad5a8bb372317bb910c243cf9b 16320 staden_2.0.0+b11-4.debian.tar.xz Files: ae59565ded12242c4c2728fbf2e185a7 4754651 staden_2.0.0+b11.orig.tar.gz 093b8c4367dd3b2977120273eaa0f75e 16320 staden_2.0.0+b11-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlw54gwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG9DhAAnFWvKDs2qJMqQoZlSM4Q6xiH4mjoBlTM AjwuqiLxvIeTx0aQkXlgve93BdytZEWCKVwJllM1+smoJUIky4vcZsITyAnX9/ls 2AEEMYa4y8RDL5amCvSlIdDPyNr3Fda1hS+BDMZnPQwCMubsmbjp2JaqCw+fPuN+ zgs2gJBbKC8qGZbi1Bfx4q+KKqDWv46QTeMHEn5fqaiW4ruMRTnpxHCWR2Za/Lhj ZgtJU8Y04FXFIZZrS/5NGhWS7g7IYW1mPYtNrpu3EqiiW3t9pKb0A9uI8Dd7y8Pb 9tvZwGelO7hc8kkVaRZ+OfejoojRsIT2uQWQeLkn+t3zlWHI0dk/whgB/eJWay9s yEc4KRucJw5nznw+5qAFSUFZ0RA4t5AWFnXClRXvyJTJfJ95jz8GmXLuQwVe6qPZ pbEqF22FHxbAinFLD9GeIuyrM+L4YjHqMqoyNbD2Zoo1VHWlSRCJ5rjnfZLcsOkA DxC7IrjGyO52q8V/MP+DVE8kYFO9FODk9tqcjikyzE15C0n9c1b09d2mYdJ9e86w deh7l0GlVqqP9pNuaI1DgIO2BH4tJECTECBfeVa14J30pXQ5MI/ON55QtN40czV4 wtdLqWyODg5IaB4M/3F0yErOJpd3xdfneL1prf7tnUERFfYCwRn6/vL5lYZiwz0g EIZMrx/4eqk= =xmBo -----END PGP SIGNATURE----- Mon Jun 21 20:34:00 UTC 2021 I: Checking whether the package is not for us Mon Jun 21 20:34:00 UTC 2021 I: Starting 1st build on remote node ionos2-i386.debian.net. Mon Jun 21 20:34:00 UTC 2021 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Mon Jun 21 20:42:12 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 21 08:34:07 -12 2021 I: pbuilder-time-stamp: 1624307647 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: using eatmydata during job I: Copying source file I: copying [staden_2.0.0+b11-4.dsc] I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.pFstxVqZ/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/2746/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='e5e0aaa722bd4df988a309aa483af880' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2746' 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.MCri6yuwAO/pbuilderrc_HO3u --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/b1 --logfile b1/build.log staden_2.0.0+b11-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux I: ls -l /bin total 5808 -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 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 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 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 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 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 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 19 21:25 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 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/2746/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), libstaden-read-dev (>= 1.14.6), itcl3-dev, itk3-dev, zlib1g-dev, libbz2-dev, liblzma-dev, tcl-dev, tk-dev, tklib, libpng-dev, libncurses5-dev, iwidgets4, libcurl4-gnutls-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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 tilix 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 40.6 MB of archives. After unpacking 134 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libtcl8.6 i386 8.6.11+dfsg-1 [1082 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libxft2 i386 2.3.2-2 [58.2 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 x11-common all 1:7.7+22 [252 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libtk8.6 i386 8.6.11-2 [825 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 itcl3 i386 3.4.3-3.1 [57.2 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 itk3 i386 3.4.2-3.1 [31.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 tcl8.6 i386 8.6.11+dfsg-1 [124 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 tcl8.6-dev i386 8.6.11+dfsg-1 [1110 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 tcl i386 8.6.11+1 [5788 B] Get: 60 http://deb.debian.org/debian bullseye/main i386 tcl-dev i386 8.6.11+1 [8348 B] Get: 61 http://deb.debian.org/debian bullseye/main i386 itcl3-dev i386 3.4.3-3.1 [15.6 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 x11proto-dev all 2020.1-1 [594 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 x11proto-core-dev all 2020.1-1 [3404 B] Get: 65 http://deb.debian.org/debian bullseye/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 69 http://deb.debian.org/debian bullseye/main i386 libxcb1-dev i386 1.14-3 [181 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libx11-dev i386 2:1.7.1-1 [875 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 x11proto-xext-dev all 2020.1-1 [3404 B] Get: 72 http://deb.debian.org/debian bullseye/main i386 libxext-dev i386 2:1.3.3-1.1 [111 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 x11proto-scrnsaver-dev all 2020.1-1 [3412 B] Get: 74 http://deb.debian.org/debian bullseye/main i386 libxss-dev i386 1:1.2.3-1 [23.8 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2 [147 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libbrotli-dev i386 1.0.9-2+b2 [287 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libpng-dev i386 1.6.37-3 [307 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libfreetype-dev i386 2.10.4+dfsg-1 [588 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libfreetype6-dev i386 2.10.4+dfsg-1 [82.4 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 uuid-dev i386 2.36.1-7 [99.2 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libfontconfig-dev i386 2.13.1-4.2 [383 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libfontconfig1-dev i386 2.13.1-4.2 [238 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libxrender-dev i386 1:0.9.10-1 [42.2 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libxft-dev i386 2.3.2-2 [70.4 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 tk8.6 i386 8.6.11-2 [72.5 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 tk8.6-dev i386 8.6.11-2 [860 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 tk i386 8.6.11+1 [5828 B] Get: 90 http://deb.debian.org/debian bullseye/main i386 tk-dev i386 8.6.11+1 [5644 B] Get: 91 http://deb.debian.org/debian bullseye/main i386 itk3-dev i386 3.4.2-3.1 [5580 B] Get: 92 http://deb.debian.org/debian bullseye/main i386 iwidgets4 all 4.1.1-2.1 [195 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.2 [367 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.2 [471 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libhtscodecs2 i386 0.5-3 [53.1 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libhtscodecs-dev i386 0.5-3 [2518 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 libncurses-dev i386 6.2+20201114-2 [373 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libncurses5-dev i386 6.2+20201114-2 [932 B] Get: 109 http://deb.debian.org/debian bullseye/main i386 libstaden-read14 i386 1.14.13-4 [288 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libstaden-read-dev i386 1.14.13-4 [370 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 tklib all 0.7+20210111-1 [1280 kB] Fetched 40.6 MB in 5s (7398 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 ... 19675 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../001-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../003-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libtcl8.6:i386. Preparing to unpack .../005-libtcl8.6_8.6.11+dfsg-1_i386.deb ... Unpacking libtcl8.6:i386 (8.6.11+dfsg-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../006-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../007-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../008-libpng16-16_1.6.37-3_i386.deb ... Unpacking libpng16-16:i386 (1.6.37-3) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../009-libfreetype6_2.10.4+dfsg-1_i386.deb ... Unpacking libfreetype6:i386 (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:i386. Preparing to unpack .../014-libfontconfig1_2.13.1-4.2_i386.deb ... Unpacking libfontconfig1:i386 (2.13.1-4.2) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../015-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../016-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../017-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../018-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../019-libxcb1_1.14-3_i386.deb ... Unpacking libxcb1:i386 (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:i386. Preparing to unpack .../021-libx11-6_2%3a1.7.1-1_i386.deb ... Unpacking libx11-6:i386 (2:1.7.1-1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../022-libxrender1_1%3a0.9.10-1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1) ... Selecting previously unselected package libxft2:i386. Preparing to unpack .../023-libxft2_2.3.2-2_i386.deb ... Unpacking libxft2:i386 (2.3.2-2) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../024-libxext6_2%3a1.3.3-1.1_i386.deb ... Unpacking libxext6:i386 (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:i386. Preparing to unpack .../026-libxss1_1%3a1.2.3-1_i386.deb ... Unpacking libxss1:i386 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:i386. Preparing to unpack .../027-libtk8.6_8.6.11-2_i386.deb ... Unpacking libtk8.6:i386 (8.6.11-2) ... Selecting previously unselected package itcl3:i386. Preparing to unpack .../028-itcl3_3.4.3-3.1_i386.deb ... Unpacking itcl3:i386 (3.4.3-3.1) ... Selecting previously unselected package itk3:i386. Preparing to unpack .../029-itk3_3.4.2-3.1_i386.deb ... Unpacking itk3:i386 (3.4.2-3.1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../030-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../031-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../032-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../033-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../034-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../035-m4_1.4.18-5_i386.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_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../046-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../047-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../048-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../049-libicu67_67.1-6_i386.deb ... Unpacking libicu67:i386 (67.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../050-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.21-4_i386.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:i386. Preparing to unpack .../055-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../056-tcl8.6_8.6.11+dfsg-1_i386.deb ... Unpacking tcl8.6 (8.6.11+dfsg-1) ... Selecting previously unselected package tcl8.6-dev:i386. Preparing to unpack .../057-tcl8.6-dev_8.6.11+dfsg-1_i386.deb ... Unpacking tcl8.6-dev:i386 (8.6.11+dfsg-1) ... Selecting previously unselected package tcl. Preparing to unpack .../058-tcl_8.6.11+1_i386.deb ... Unpacking tcl (8.6.11+1) ... Selecting previously unselected package tcl-dev:i386. Preparing to unpack .../059-tcl-dev_8.6.11+1_i386.deb ... Unpacking tcl-dev:i386 (8.6.11+1) ... Selecting previously unselected package itcl3-dev:i386. Preparing to unpack .../060-itcl3-dev_3.4.3-3.1_i386.deb ... Unpacking itcl3-dev:i386 (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:i386. Preparing to unpack .../064-libxau-dev_1%3a1.0.9-1_i386.deb ... Unpacking libxau-dev:i386 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:i386. 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Setting up libpsl5:i386 (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:i386 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (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:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libpthread-stubs0-dev:i386 (0.4-1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up libhtscodecs-dev:i386 (0.5-3) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libexpat1-dev:i386 (2.2.10-2) ... Setting up libx11-data (2:1.7.1-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up uuid-dev:i386 (2.36.1-7) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up libtcl8.6:i386 (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:i386 (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libbrotli-dev:i386 (1.0.9-2+b2) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up tcl8.6 (8.6.11+dfsg-1) ... Setting up libncurses-dev:i386 (6.2+20201114-2) ... Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libxau-dev:i386 (1:1.0.9-1) ... Setting up libtool (2.4.6-15) ... Setting up tcl8.6-dev:i386 (8.6.11+dfsg-1) ... Setting up libpng-dev:i386 (1.6.37-3) ... Setting up itcl3:i386 (3.4.3-3.1) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.2) ... Setting up libcurl4-gnutls-dev:i386 (7.74.0-1.2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxdmcp-dev:i386 (1:1.1.2-3) ... Setting up libfreetype6:i386 (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 (1.11.0-1) ... 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:i386 (6.2+20201114-2) ... Setting up libx11-6:i386 (2:1.7.1-1) ... Setting up libstaden-read14:i386 (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:i386 (3.4.3-3.1) ... Setting up libxcb1-dev:i386 (1.14-3) ... Setting up libxrender1:i386 (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:i386 (2:1.7.1-1) ... Setting up libxext6:i386 (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:i386 (2.10.4+dfsg-1) ... Setting up dh-autoreconf (20) ... Setting up tcl-dev:i386 (8.6.11+1) ... Setting up libxext-dev:i386 (2:1.3.3-1.1) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up libxrender-dev:i386 (1:0.9.10-1) ... Setting up libxft2:i386 (2.3.2-2) ... Setting up libtk8.6:i386 (8.6.11-2) ... Setting up debhelper (13.3.4) ... Setting up libxss-dev:i386 (1:1.2.3-1) ... Setting up libfreetype6-dev:i386 (2.10.4+dfsg-1) ... Setting up itk3:i386 (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:i386 (2.13.1-4.2) ... Setting up tk (8.6.11+1) ... Setting up libxft-dev:i386 (2.3.2-2) ... Setting up libfontconfig1-dev:i386 (2.13.1-4.2) ... Setting up tklib (0.7+20210111-1) ... Setting up tk8.6-dev:i386 (8.6.11-2) ... Setting up itk3-dev:i386 (3.4.2-3.1) ... Setting up tk-dev:i386 (8.6.11+1) ... Processing triggers for libc-bin (2.31-12) ... 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 dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/staden-2.0.0+b11' make spotless || true make[2]: Entering directory '/build/staden-2.0.0+b11' make[2]: *** No rule to make target 'spotless'. Stop. make[2]: Leaving directory '/build/staden-2.0.0+b11' rm -f config.log config.status rm -f Makefile shlib.conf staden_config.h system.mk find -name debian -prune -o -name .dir -exec rm '{}' ';' make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf 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/i386-linux-gnu \ --with-itk=/usr/lib/tcltk/i386-linux-gnu ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-itcl=/usr/lib/tcltk/i386-linux-gnu --with-itk=/usr/lib/tcltk/i386-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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-4.19.0-17-686-pae checking for ar... ar checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... long long checking for struct dirent64... no checking for struct stat64... no checking for open64... yes checking for lseek64... yes checking for off64_t... no checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include/tcl8.6 checking for Tcl private include files... Using srcdir found in tclConfig.sh: /usr/include/tcl8.6/tcl-private checking for Tk public headers... /usr/include/tcl8.6 checking for Tk private include files... Using srcdir found in tkConfig.sh: /usr/include/tcl8.6/tk-private checking tklib directory... yes (/usr/share/tcltk/tklib0.7) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/i386-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/i386-linux-gnu/itk3.4) configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/share/tcltk/tklib0.7 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/i386-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/i386-linux-gnu/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_auto_build make -j10 make[1]: Entering directory '/build/staden-2.0.0+b11' cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts all cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data all cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc all make[2]: Entering directory '/build/staden-2.0.0+b11/scripts' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev all make[2]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j10 --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: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/data' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j10 --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 -j10 --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/trev' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/primer3' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[2]: warning: -j10 forced in submake: resetting jobserver mode. /build/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' /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 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 -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 Nothing to build for spin_emboss. Nothing to build for data. make[2]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' gcc -g -O2 -fdebug-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 make[2]: Leaving directory '/build/staden-2.0.0+b11/data' 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 make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3' 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 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 crash.o -c crash.c gcc -g -O2 -fdebug-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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 mkdir -p /build/staden-2.0.0+b11/lib 2>/dev/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/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 -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 primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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, 56512728] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:867, from primer3_main.c:7: /usr/include/i386-linux-gnu/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/./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 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/i386-linux-gnu/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 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 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/i386-linux-gnu/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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c parse_db.c: In function 'parse_entry': parse_db.c:234:52: 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/i386-linux-gnu/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 -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 -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all make[2]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j10 --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/text_utils' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/alf' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi all cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j10 --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/abi' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba all cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j10 --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/g' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/eba' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j10 --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/init_exp' make[2]: warning: -j10 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 make[2]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j10 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/./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/./alf -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins 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/./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 make[2]: Entering directory '/build/staden-2.0.0+b11/hetins' make[2]: warning: -j10 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/./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/./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/./init_exp -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./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/./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/./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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./get_scf_field -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./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/./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 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/./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/./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/./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 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) ; | ^~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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/./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/./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/./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/./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 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 -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 make[2]: Leaving directory '/build/staden-2.0.0+b11/text_utils' 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sheet.o -c sheet.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib/i386-linux-gnu -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/i386-linux-gnu -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 tkSheet.o -c tkSheet.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/alf' gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o get_scf_field get_scf_field.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -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 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/./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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 postscript.o -c postscript.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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/./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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 capture.o -c capture.c make[2]: Leaving directory '/build/staden-2.0.0+b11/init_exp' 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 make[2]: Leaving directory '/build/staden-2.0.0+b11/eba' make[2]: Leaving directory '/build/staden-2.0.0+b11/abi' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -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 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 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/i386-linux-gnu/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 -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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container.o -c container.c make[2]: Leaving directory '/build/staden-2.0.0+b11/g' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -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 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 tcl_io_lib.o -c tcl_io_lib.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 primer3_core primer3_main.o -lprimer3 -lm -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' 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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j10 --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: -j10 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 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 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/i386-linux-gnu/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 -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 spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin all make[2]: Entering directory '/build/staden-2.0.0+b11/spin' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all make[2]: Entering directory '/build/staden-2.0.0+b11/mutlib' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip all cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j10 --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/screen_seq' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops all cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j10 --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/qclip' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/stops' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j10 --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/make_weights' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/find_renz' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/gap5' make[2]: warning: -j10 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 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/./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/./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/./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 seq_reg_cmds.o -c seq_reg_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 align.o -c align.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 raster_cmds.o -c raster_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/./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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c g++ -g -O2 -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/./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/./vector_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 caller_base.o -c caller_base.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 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 seqed.o -c seqed.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/find_renz' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./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 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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 tkSeqedNames.o -c tkSeqedNames.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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -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 tagarray.o -c tagarray.cpp gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -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 seqedInterface.o -c seqedInterface.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 trace.o -c trace.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_library.o -c tg_library.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 validate.o -c validate.cpp make[2]: Leaving directory '/build/staden-2.0.0+b11/make_weights' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c make[2]: Leaving directory '/build/staden-2.0.0+b11/stops' make[2]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' 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 make[2]: Leaving directory '/build/staden-2.0.0+b11/qclip' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/i386-linux-gnu/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/i386-linux-gnu/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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c g++ -g -O2 -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 readpam.o -c readpam.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_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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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++ -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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o screen_seq screen_seq.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 tracediff_helper.o -c tracediff_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 tracediff_mutations.o -c tracediff_mutations.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_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 sip_find_identity.o -c sip_find_identity.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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 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); | ^~~~~~~~~~~~~~~~~~~~~~ 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 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 make[2]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' 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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c g++ -g -O2 -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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 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 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 -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./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 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 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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./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 make[2]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -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/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/spin' 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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); | ^ 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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/mutlib' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all make[2]: Entering directory '/build/staden-2.0.0+b11/gap4' make[2]: warning: -j10 forced in submake: resetting jobserver mode. cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j10 --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/tracediff' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/mutscan' make[2]: warning: -j10 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 export_snps.o -c export_snps.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/./tracediff -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 IO2.o -c IO2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/i386-linux-gnu/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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 interval_tree.o -c interval_tree.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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm 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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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 make[2]: Leaving directory '/build/staden-2.0.0+b11/tracediff' gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/i386-linux-gnu/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 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 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 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 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 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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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 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/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/i386-linux-gnu/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/i386-linux-gnu/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); | ^~~~~~~~~~~~~ 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/i386-linux-gnu/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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/i386-linux-gnu/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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 -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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc 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/i386-linux-gnu/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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/i386-linux-gnu/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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 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/i386-linux-gnu/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 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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 /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 edExtend.o -c edExtend.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h: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/i386-linux-gnu/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 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 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 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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o copy_db gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o copy_db.o copy_db_main.o text-io-reg.o io_utils.o io_handle.o -lg -ltext_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm 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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert all make[2]: Entering directory '/build/staden-2.0.0+b11/prefinish' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/haplo' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/copy_reads' make[2]: warning: -j10 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/convert' make[2]: warning: -j10 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/./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/./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/./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/./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/./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/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./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/./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/./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 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/./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_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/./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 gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./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/./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 main.c: In function 'get_db': main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-2.0.0+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/./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 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/i386-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/i386-linux-gnu/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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -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 staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz 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/i386-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' 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/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap 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/i386-linux-gnu -ltk8.6 -L/usr/lib/i386-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' 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 -j10 install DESTDIR=/build/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/staden-2.0.0+b11' mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/bin mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/doc mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/share/man cp shlib.conf /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp ./staden.profile /build/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/staden-2.0.0+b11' cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j10 --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 -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev install cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install make[4]: Entering directory '/build/staden-2.0.0+b11/primer3' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/trev' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/primer3/src' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install make[4]: Entering directory '/build/staden-2.0.0+b11/Misc' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts install cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data install make[4]: Entering directory '/build/staden-2.0.0+b11/pregap4' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/scripts' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/data' make[4]: warning: -j10 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' /build/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /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/etc/alus cp /build/staden-2.0.0+b11/./scripts/assemble4 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 cp /build/staden-2.0.0+b11/lib/libmisc.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/lib/libprimer3.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden install trev /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3' cp /build/staden-2.0.0+b11/./data/alus/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/staden-2.0.0+b11/./spin_emboss/*.tcl /build/staden-2.0.0+b11/./spin_emboss/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss make[4]: Leaving directory '/build/staden-2.0.0+b11/Misc' make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev make[4]: Entering directory '/build/staden-2.0.0+b11/tk_utils' make[4]: warning: -j10 forced in submake: resetting jobserver mode. 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/./trev/trev.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cp /build/staden-2.0.0+b11/./pregap4/*.tcl /build/staden-2.0.0+b11/./pregap4/widget_licence /build/staden-2.0.0+b11/./pregap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 make[4]: Entering directory '/build/staden-2.0.0+b11/abi' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/text_utils' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf install cp /build/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j10 --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/alf' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/g' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/./trev/trevrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp getABISampleName getABIcomment getABIdate getABIfield /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libtk_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/./scripts/splitseq_da /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Leaving directory '/build/staden-2.0.0+b11/trev' cp /build/staden-2.0.0+b11/./scripts/staden_help /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j10 --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/lib/libg.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Entering directory '/build/staden-2.0.0+b11/eba' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/text_utils' cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/scripts' make[4]: Leaving directory '/build/staden-2.0.0+b11/g' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils make[4]: Leaving directory '/build/staden-2.0.0+b11/alf' 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 cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j10 --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 cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins install make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cp eba /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/hetins' make[4]: warning: -j10 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/abi' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl make[4]: Leaving directory '/build/staden-2.0.0+b11/eba' cp /build/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cp: cannot stat '/build/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory make[4]: [/build/staden-2.0.0+b11/./spin_emboss/Makefile:30: install] Error 1 (ignored) cp /build/staden-2.0.0+b11/./spin_emboss/emboss_menu /build/staden-2.0.0+b11/./spin_emboss/spin_embossrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' cp hetins /build/staden-2.0.0+b11/debian/tmp/usr/bin cp init_exp /build/staden-2.0.0+b11/debian/tmp/usr/bin cp get_scf_field /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/init_exp' make[4]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' 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/modules mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cp /build/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates cp: cannot stat '/build/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory make[4]: [/build/staden-2.0.0+b11/./pregap4/Makefile:42: install] Error 1 (ignored) cp /build/staden-2.0.0+b11/./pregap4/naming_schemes/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-2.0.0+b11/./tk_utils/stash /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./pregap4/pregap4rc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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/pregap4' make[4]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' make[4]: warning: -j10 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/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j10 --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 -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin install cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip install make[4]: Entering directory '/build/staden-2.0.0+b11/spin' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/mutlib' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/vector_clip' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/screen_seq' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/qclip' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j10 --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 -j10 --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: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/stops' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j10 --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/find_renz' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j10 --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]: Entering directory '/build/staden-2.0.0+b11/make_weights' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cp vector_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp screen_seq /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libmutlib.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin install spin /build/staden-2.0.0+b11/debian/tmp/usr/bin cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin cp find_renz /build/staden-2.0.0+b11/debian/tmp/usr/bin cp polyA_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp make_weights /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/stops' make[4]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' make[4]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' make[4]: Leaving directory '/build/staden-2.0.0+b11/find_renz' make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/make_weights' make[4]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' 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]: Leaving directory '/build/staden-2.0.0+b11/mutlib' cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff 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/gap4' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/tracediff' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install install gap5 /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/staden-2.0.0+b11/mutscan' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cp tracediff /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 make[4]: Leaving directory '/build/staden-2.0.0+b11/tracediff' cp mutscan /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/mutscan' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-2.0.0+b11/./data/gcodes/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-2.0.0+b11/./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/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/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/./data/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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/./spin/*.wts /build/staden-2.0.0+b11/./spin/niprc /build/staden-2.0.0+b11/./spin/siprc /build/staden-2.0.0+b11/./spin/spinrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/spin' 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/./data/m13mp18_primers /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc 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/./data/vector_primer /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./data/pam250 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/lib/libgap5.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/data' cp /build/staden-2.0.0+b11/lib/libgap.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp tg_index.bin /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 tg_index /build/staden-2.0.0+b11/debian/tmp/usr/bin install gap5_cmd /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/gap5' cp /build/staden-2.0.0+b11/./gap4/GTAGDB /build/staden-2.0.0+b11/./gap4/NOTEDB /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/cap2rc /build/staden-2.0.0+b11/./gap4/cap3rc /build/staden-2.0.0+b11/./gap4/fak2rc /build/staden-2.0.0+b11/./gap4/phraprc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/*.bitmap /build/staden-2.0.0+b11/./gap4/*.gif /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/gap4' cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert install cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j10 --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 -j10 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo install make[4]: Entering directory '/build/staden-2.0.0+b11/convert' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/prefinish' make[4]: warning: -j10 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/haplo' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j10 --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/copy_reads' make[4]: warning: -j10 forced in submake: resetting jobserver mode. cp staden_convert /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 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 mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/convert' cp /build/staden-2.0.0+b11/lib/libhaplo.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden cp /build/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/staden-2.0.0+b11/./copy_reads/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads cp /build/staden-2.0.0+b11/./haplo/haplorc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/haplo' cp /build/staden-2.0.0+b11/lib/libcopy_reads.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/staden 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]: 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/i386-linux-gnu/staden install prefinish /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./prefinish/finish_sanger /build/staden-2.0.0+b11/./prefinish/finish_cDNA /build/staden-2.0.0+b11/./prefinish/finish_cDNA_ends_only \ /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-2.0.0+b11/./prefinish/rules/*.rule /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-2.0.0+b11/./prefinish/prefinishrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/prefinish' make[3]: Leaving directory '/build/staden-2.0.0+b11' make[2]: Leaving directory '/build/staden-2.0.0+b11' # Remove file causing lintian errors that is targeting at windows find debian -name help_windows.tcl -delete # Remove some empty directories find debian -type d -empty -name acdtcl -delete find debian -type d -empty -name templates -delete # Build system is not prepared for multi-arch mv /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu/* /build/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/staden-2.0.0+b11/debian/tmp/usr/lib/i386-linux-gnu make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-4_all.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_i386.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../staden_2.0.0+b11-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/2746 and its subdirectories I: Current time: Mon Jun 21 08:42:11 -12 2021 I: pbuilder-time-stamp: 1624308131 Mon Jun 21 20:42:13 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Mon Jun 21 20:42:13 UTC 2021 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Mon Jun 21 20:43:11 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. Mon Jun 21 20:43:12 UTC 2021 I: staden_2.0.0+b11-4_i386.changes: Format: 1.8 Date: Sat, 12 Jan 2019 11:40:05 +0100 Source: staden Binary: staden staden-common staden-dbgsym Architecture: all i386 Version: 2.0.0+b11-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: staden - DNA sequence assembly (Gap4/Gap5), editing and analysis tools staden-common - Architecture independent files for Staden Closes: 918272 Changes: staden (2.0.0+b11-4) unstable; urgency=medium . * Build-Depends: s/libcurl4-openssl-dev/libcurl4-gnutls-dev/ Closes: #918272 * debhelper 12 * Standards-Version: 4.3.0 * Secure URI in copyright format * Remove trailing whitespace in debian/copyright Checksums-Sha1: a90429ac5553c46efdd1e29da25463e76f6bbeb3 1971592 staden-common_2.0.0+b11-4_all.deb 39a3e964755834ce3a45decd70040ef53bd19753 3528336 staden-dbgsym_2.0.0+b11-4_i386.deb 5852e7a5581c0830bd942be0fcd5989548a37f06 7655 staden_2.0.0+b11-4_i386.buildinfo 3779fc78e714a07e0529b85489997610ee2a9b57 1732016 staden_2.0.0+b11-4_i386.deb Checksums-Sha256: 59967bbcb023cd3a99a37893e2ecf9c8854293837d788c955b3597785bead875 1971592 staden-common_2.0.0+b11-4_all.deb 1e3c61e02792b38a4f5ff6fbe25865f1c665ed28b07f1d00df9e5e6e342f186c 3528336 staden-dbgsym_2.0.0+b11-4_i386.deb a9c7745d2469595669a2249dd455ba1e512da79594480440d302b6f9d4930066 7655 staden_2.0.0+b11-4_i386.buildinfo 4bb1c8eb851d6028949548d5699144dc65ea22da129f9bd06c33eb7739c1fd4d 1732016 staden_2.0.0+b11-4_i386.deb Files: 279513f7035dd4a3e29e0b93065a888e 1971592 science optional staden-common_2.0.0+b11-4_all.deb 09ce551b341411694aacaf7e85a3f5ba 3528336 debug optional staden-dbgsym_2.0.0+b11-4_i386.deb e3da929aff0196cff38b7bda0feef879 7655 science optional staden_2.0.0+b11-4_i386.buildinfo 753f133846a457c3d3a6ae70ae4755ac 1732016 science optional staden_2.0.0+b11-4_i386.deb Mon Jun 21 20:43:13 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/staden_2.0.0+b11-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/staden_2.0.0+b11-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/staden_2.0.0+b11-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/b1/staden_2.0.0+b11-4_i386.changes /srv/reproducible-results/rbuild-debian/tmp.MCri6yuwAO/b2/staden_2.0.0+b11-4_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.370s) 0.370s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.088s) 0.088s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jun 21 20:43:15 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Mon Jun 21 20:43:15 UTC 2021 I: staden from bullseye built successfully and reproducibly on i386. Mon Jun 21 20:43:17 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jun 21 20:43:17 UTC 2021 I: Submitting 12K b1/staden_2.0.0+b11-4_i386.buildinfo.asc Mon Jun 21 20:43:19 UTC 2021 I: Submitting 12K b2/staden_2.0.0+b11-4_i386.buildinfo.asc Mon Jun 21 20:43:20 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jun 21 20:43:20 UTC 2021 I: Done submitting .buildinfo files. Mon Jun 21 20:43:20 UTC 2021 I: Removing signed staden_2.0.0+b11-4_i386.buildinfo.asc files: removed './b1/staden_2.0.0+b11-4_i386.buildinfo.asc' removed './b2/staden_2.0.0+b11-4_i386.buildinfo.asc'