Diff of the two buildlogs: -- --- b1/build.log 2023-07-12 17:19:44.350354648 +0000 +++ b2/build.log 2023-07-12 17:44:18.144981144 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 12 05:14:46 -12 2023 -I: pbuilder-time-stamp: 1689182086 +I: Current time: Thu Jul 13 07:20:27 +14 2023 +I: pbuilder-time-stamp: 1689182427 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 12 00:48:12 2019 -12 +gpgv: Signature made Sun Jan 13 02:48:12 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -36,135 +36,167 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6101/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 13 07:21 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='41f6f39a81a94e7a83564656379fa18c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='6101' - PS1='# ' - PS2='> ' + INVOCATION_ID=c42ba6f5bda741e6aa9f5b576e106ff3 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=15285 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/r-b-build.wshphEcJ/pbuilderrc_96bH --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wshphEcJ/b1 --logfile b1/build.log staden_2.0.0+b11-4.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wshphEcJ/pbuilderrc_zaQc --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wshphEcJ/b2 --logfile b2/build.log staden_2.0.0+b11-4.dsc' + SUDO_GID=116 + SUDO_UID=112 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1a 6.1.0-10-arm64 #1 SMP Debian 6.1.37-1 (2023-07-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-10-armmp #1 SMP Debian 6.1.37-1 (2023-07-03) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 2023 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/6101/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 2023 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 13 07:21 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -333,7 +365,7 @@ Get: 105 http://deb.debian.org/debian bookworm/main armhf libstaden-read14 armhf 1.14.15-1 [231 kB] Get: 106 http://deb.debian.org/debian bookworm/main armhf libstaden-read-dev armhf 1.14.15-1 [309 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf tklib all 0.8~20230222-1 [1406 kB] -Fetched 38.0 MB in 3s (14.2 MB/s) +Fetched 38.0 MB in 8s (4560 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libtcl8.6:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19288 files and directories currently installed.) @@ -783,7 +815,11 @@ fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/staden-2.0.0+b11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden_2.0.0+b11-4_source.changes +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/staden-2.0.0+b11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../staden_2.0.0+b11-4_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-4 dpkg-buildpackage: info: source distribution unstable @@ -1037,7 +1073,7 @@ 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-6.1.0-10-arm64 +checking system version... Linux-6.1.0-10-armmp checking for ar... ar checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no @@ -1092,71 +1128,72 @@ ---------------------------------------------------------------------- make[1]: Leaving directory '/build/staden-2.0.0+b11' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/staden-2.0.0+b11' -cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc all -cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev all -cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all -make[2]: Entering directory '/build/staden-2.0.0+b11/Misc' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev all +cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all +cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc all make[2]: Entering directory '/build/staden-2.0.0+b11/trev' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src all make[2]: Entering directory '/build/staden-2.0.0+b11/primer3' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -make[2]: Nothing to be done for 'all'. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/Misc' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/primer3/src' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/trev' +make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o crash.o -c crash.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o date.o -c date.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c -cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src all -cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all -make[2]: Entering directory '/build/staden-2.0.0+b11/pregap4' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -make[2]: Entering directory '/build/staden-2.0.0+b11/primer3/src' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -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 +cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c -/build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' -/build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c -Nothing to build for Pregap4. -make[2]: Leaving directory '/build/staden-2.0.0+b11/pregap4' -cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all +cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all +make[2]: Entering directory '/build/staden-2.0.0+b11/pregap4' +gcc -g -O2 -ffile-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]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +/build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' +/build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' +Nothing to build for Pregap4. +make[2]: Leaving directory '/build/staden-2.0.0+b11/pregap4' Nothing to build for spin_emboss. make[2]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c -cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts all -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts all +cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data all make[2]: Entering directory '/build/staden-2.0.0+b11/scripts' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-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]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/data' +make[2]: warning: -j4 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' -Nothing to build for scripts. -make[2]: Leaving directory '/build/staden-2.0.0+b11/scripts' -cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data all -make[2]: Entering directory '/build/staden-2.0.0+b11/data' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. /build/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +Nothing to build for scripts. Nothing to build for data. make[2]: Leaving directory '/build/staden-2.0.0+b11/data' +make[2]: Leaving directory '/build/staden-2.0.0+b11/scripts' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shell.o -c shell.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o error.o -c error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -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 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array.o -c array.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o locks.o -c locks.c @@ -1164,6 +1201,7 @@ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c parse_db.c: In function 'parse_entry': parse_db.c:234:66: warning: '%s' directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); @@ -1179,37 +1217,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o boulder_input.o -c boulder_input.c mkdir -p /build/staden-2.0.0+b11/lib 2>/dev/null touch /build/staden-2.0.0+b11/lib/.dir -gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm -make[2]: Leaving directory '/build/staden-2.0.0+b11/Misc' -cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all -make[2]: Entering directory '/build/staden-2.0.0+b11/text_utils' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all -make[2]: Entering directory '/build/staden-2.0.0+b11/tk_utils' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cli_arg.o -c cli_arg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXkeylist.o -c tclXkeylist.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXutil.o -c tclXutil.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc mkdir -p /build/staden-2.0.0+b11/lib 2>/dev/null touch /build/staden-2.0.0+b11/lib/.dir gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/text_utils' -cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi all -make[2]: Entering directory '/build/staden-2.0.0+b11/abi' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_debug.o -c tcl_debug.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o misc.o -c misc.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c 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), \ @@ -1223,9 +1235,27 @@ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ +gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm +make[2]: Leaving directory '/build/staden-2.0.0+b11/Misc' +cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all +cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all +cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi all +make[2]: Entering directory '/build/staden-2.0.0+b11/tk_utils' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/text_utils' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/abi' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cli_arg.o -c cli_arg.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXkeylist.o -c tclXkeylist.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXutil.o -c tclXutil.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./abi -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c primer3_main.c: In function 'boulder_print_oligos': primer3_main.c:416:32: warning: '%d' directive writing between 1 and 8 bytes into a region of size 2 [-Wformat-overflow=] 416 | else sprintf(suffix, "_%d", i); @@ -1244,6 +1274,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_debug.o -c tcl_debug.c primer3_main.c: In function 'main': primer3_main.c:234:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); @@ -1263,19 +1296,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output.o -c text_output.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/text_utils' +cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf all +make[2]: Entering directory '/build/staden-2.0.0+b11/alf' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./alf -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o misc.o -c misc.c gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIcomment abiIO.o getABIcomment.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -lmisc -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sheet.o -c sheet.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/abi' -cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf all -make[2]: Entering directory '/build/staden-2.0.0+b11/alf' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./alf -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 alfsplit.c: In function 'main': alfsplit.c:347:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | fread (buf,512,1,inData) ; @@ -1290,6 +1320,7 @@ alfsplit.c:135:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 135 | fread (junk,70,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 alfsplit.c: In function 'main': alfsplit.c:312:29: warning: '%s' directive writing up to 2559 bytes into a region of size 25 [-Wformat-overflow=] 312 | sprintf (fname,"%sALF",name[i]) ; @@ -1305,43 +1336,71 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet.o -c tkSheet.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRaster.o -c tkRaster.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 getABIfield abiIO.o getABIfield.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o alfsplit alfsplit.o -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/alf' -cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g all +cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g all make[2]: Entering directory '/build/staden-2.0.0+b11/g' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet_common.o -c tkSheet_common.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/abi' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba all +make[2]: Entering directory '/build/staden-2.0.0+b11/eba' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o 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 primer3_core primer3_main.o -lprimer3 -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o postscript.o -c postscript.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba all -make[2]: Entering directory '/build/staden-2.0.0+b11/eba' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./eba -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o split.o -c split.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTrace.o -c tkTrace.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceComp.o -c tkTraceComp.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceIO.o -c tkTraceIO.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet_common.o -c tkSheet_common.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 eba qual.o conf.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceDisp.o -c tkTraceDisp.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/eba' -cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all +cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all make[2]: Entering directory '/build/staden-2.0.0+b11/init_exp' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./init_exp -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o split.o -c split.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTrace.o -c tkTrace.c +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceComp.o -c tkTraceComp.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm +make[2]: Leaving directory '/build/staden-2.0.0+b11/init_exp' +cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all +make[2]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./get_scf_field -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' +cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins all +make[2]: Entering directory '/build/staden-2.0.0+b11/hetins' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./hetins -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/g' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 get_scf_field get_scf_field.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o capture.o -c capture.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' +capture.c: In function 'tcl_capture': +capture.c:33:14: warning: implicit declaration of function 'mkostemp'; did you mean 'mkstemp'? [-Wimplicit-function-declaration] + 33 | fd = mkostemp(NULL, 0666); + | ^~~~~~~~ + | mkstemp +capture.c:54:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 54 | read(fd, buf, statbuf.st_size); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o canvas_box.o -c canvas_box.c tkTraceDisp.c: In function 'trace_draw_numbers': tkTraceDisp.c:746:32: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 746 | sprintf(number, "%d", cind); @@ -1357,42 +1416,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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 init_exp init_exp.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -make[2]: Leaving directory '/build/staden-2.0.0+b11/g' -cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all -make[2]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./get_scf_field -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o capture.o -c capture.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/init_exp' -cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins all -make[2]: Entering directory '/build/staden-2.0.0+b11/hetins' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./hetins -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o get_scf_field get_scf_field.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -capture.c: In function 'tcl_capture': -capture.c:33:14: warning: implicit declaration of function 'mkostemp'; did you mean 'mkstemp'? [-Wimplicit-function-declaration] - 33 | fd = mkostemp(NULL, 0666); - | ^~~~~~~~ - | mkstemp -capture.c:54:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 54 | read(fd, buf, statbuf.st_size); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o canvas_box.o -c 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 hetins hetins.o -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -make[2]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' +make[2]: Leaving directory '/build/staden-2.0.0+b11/hetins' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzyme_map.o -c restriction_enzyme_map.c -g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o hetins hetins.o -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o element_canvas.o -c element_canvas.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container.o -c container.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/hetins' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container_ruler.o -c container_ruler.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_io_lib.o -c tcl_io_lib.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' -cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all +cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all make[2]: Entering directory '/build/staden-2.0.0+b11/seq_utils' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c @@ -1402,6 +1438,21 @@ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c +sequence_formats.c: In function 'get_embl_format_seq': +sequence_formats.c:729:29: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 729 | fgets(line, loc_len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sequence_formats.c:738:33: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 738 | fgets(line, loc_len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sequence_formats.c: In function 'add_feat': +sequence_formats.c:481:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 481 | fgets(line, loc_len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 510 | fgets(line, loc_len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c 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); @@ -1417,22 +1468,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c -sequence_formats.c: In function 'get_embl_format_seq': -sequence_formats.c:729:29: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 729 | fgets(line, loc_len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sequence_formats.c:738:33: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 738 | fgets(line, loc_len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sequence_formats.c: In function 'add_feat': -sequence_formats.c:481:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 481 | fgets(line, loc_len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 510 | fgets(line, loc_len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c @@ -1441,65 +1477,132 @@ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[2]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' -cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all -cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin all -cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip all +cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all +cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j4 --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/mutlib' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j4 --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: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/spin' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/vector_clip' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./screen_seq -I/build/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./vector_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp seq_reg_cmds.c: In function 'GetActiveSeqName': seq_reg_cmds.c:919:32: warning: zero-length gnu_printf format string [-Wformat-zero-length] 919 | vTcl_SetResult(interp, ""); | ^~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm +make[2]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' +cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip all +make[2]: Entering directory '/build/staden-2.0.0+b11/qclip' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qclip.o -c qclip.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm +make[2]: Leaving directory '/build/staden-2.0.0+b11/qclip' +cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all +make[2]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedUtils.o -c tkSeqedUtils.c +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' +cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops all +make[2]: Entering directory '/build/staden-2.0.0+b11/stops' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./stops -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp -make[2]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' -cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all -make[2]: Entering directory '/build/staden-2.0.0+b11/screen_seq' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./screen_seq -I/build/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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' +cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all +make[2]: Entering directory '/build/staden-2.0.0+b11/make_weights' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./make_weights -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c +sp_alignment.cpp: In function 'void sp::store_hashn(Hash*)': +sp_alignment.cpp:754:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 754 | register int i,j,n; + | ^ +sp_alignment.cpp:754:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 754 | register int i,j,n; + | ^ +sp_alignment.cpp:754:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 754 | register int i,j,n; + | ^ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm +emboss_input_funcs.c: In function 'read_emboss_data_file': +emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 402 | fgets(line, 1024, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:437:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:444:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 444 | fgets(line, 1024, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:470:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:477:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 477 | fgets(line, 1024, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:518:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c: In function 'init_emboss_stick_create': +emboss_input_funcs.c:658:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 658 | fgets(dummy1, 100, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:659:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 659 | fgets(dummy1, 100, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +emboss_input_funcs.c:660:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 660 | fgets(dummy1, 100, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:316:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 316 | sprintf(tmp, "%10d", i*10); @@ -1532,71 +1635,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c: In function 'read_emboss_data_file': -emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 402 | fgets(line, 1024, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:437:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:444:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 444 | fgets(line, 1024, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:470:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:477:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 477 | fgets(line, 1024, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:518:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c: In function 'init_emboss_stick_create': -emboss_input_funcs.c:658:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 658 | fgets(dummy1, 100, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:659:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 659 | fgets(dummy1, 100, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -emboss_input_funcs.c:660:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 660 | fgets(dummy1, 100, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp +make[2]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' +cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all +make[2]: Entering directory '/build/staden-2.0.0+b11/find_renz' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./find_renz -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm -sp_alignment.cpp: In function 'void sp::store_hashn(Hash*)': -sp_alignment.cpp:754:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 754 | register int i,j,n; - | ^ -sp_alignment.cpp:754:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 754 | register int i,j,n; - | ^ -sp_alignment.cpp:754:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 754 | register int i,j,n; - | ^ +make[2]: Leaving directory '/build/staden-2.0.0+b11/make_weights' +cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 all +make[2]: Entering directory '/build/staden-2.0.0+b11/gap5' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm +make[2]: Leaving directory '/build/staden-2.0.0+b11/find_renz' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' -cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip all -make[2]: Entering directory '/build/staden-2.0.0+b11/qclip' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o qclip.o -c qclip.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -make[2]: Leaving directory '/build/staden-2.0.0+b11/qclip' -cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all -make[2]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c sp_hash_lib.cpp: In function 'int sp::hash_word8n(char*, int*, int, int, short unsigned int*)': sp_hash_lib.cpp:57:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 57 | register int i; @@ -1610,7 +1668,6 @@ sp_hash_lib.cpp:58:38: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 sp_hash_lib.cpp:59:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 59 | register int unsigned short luword; | ^~~~~~ @@ -1654,203 +1711,243 @@ sp_hash_lib.cpp:411:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 411 | register int i; | ^ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_globals.o -c sip_globals.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -make[2]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' -cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops all -make[2]: Entering directory '/build/staden-2.0.0+b11/stops' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./stops -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sim.o -c sim.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp -make[2]: Leaving directory '/build/staden-2.0.0+b11/stops' -cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all -make[2]: Entering directory '/build/staden-2.0.0+b11/make_weights' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./make_weights -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./text_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -make[2]: Leaving directory '/build/staden-2.0.0+b11/make_weights' -cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all -make[2]: Entering directory '/build/staden-2.0.0+b11/find_renz' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 -make[2]: Leaving directory '/build/staden-2.0.0+b11/find_renz' -cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 all -make[2]: Entering directory '/build/staden-2.0.0+b11/gap5' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_cache.o -c tracealign_cache.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./spin -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libspin.so seq_reg.o seq_reg_cmds.o raster_cmds.o seq_raster.o sequtils.o seq_results.o seq_sendto.o spin_globals.o seq_plot_funcs.o seqed.o tkSeqed.o tkSeqedUtils.o tkSeqedNames.o seqed_write.o seqedInterface.o seqed_translate.o seqed_restriction_enzymes.o seqed_search.o sequence_pair_display.o emboss_input_funcs.o readpam.o compare_spans.o sip_hash.o sip_similar_spans.o sip_find_identity.o sip_quick_scan.o sip_align.o sip_globals.o sip_cmds.o sip_results.o rescan_matches.o probs.o sim.o sip_sim.o init.o nip_globals.o nip_cmds.o nip_base_comp.o nip_gene_search.o nip_trna_search.o codon_content.o nip_stop_codon.o trna_search.o splice_search.o nip_splice_search.o nip_string_search.o nip_wtmatrix_search.o nip_restriction_enzymes.o nip_canvas_box.o dinuc_freqs.o -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c make[2]: Leaving directory '/build/staden-2.0.0+b11/spin' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c cp /build/staden-2.0.0+b11/./mutlib/mutlib.def 2>&- make[2]: [/build/staden-2.0.0+b11/./mutlib/Makefile:81: /build/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libmutlib.so align.o basecall.o caller.o caller_snr.o caller_base.o caller_level.o dnatable.o muttag.o mutationtag.o mutationtag_utils.o pathutil.o peakcall.o stringlist.o tagarray.o trace.o validate.o read_matrix.o sp_align_lib.o sp_alignment.o sp_hash_lib.o sp_matrix.o tracediff.o tracediff_helper.o tracediff_mutations.o tracediff_parameters.o tracediff_validate.o tracealign.o tracealign_cache.o tracealign_helper.o tracealign_interpolate.o tracealign_preprocess.o tracealign_validate.o mutscan.o mutscan_helper.o mutscan_validate.o mutscan_analysis.o mutscan_preprocess.o mutscan_parameters.o -lseq_utils -ltk_utils -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c make[2]: Leaving directory '/build/staden-2.0.0+b11/mutlib' -cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all -cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all +cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 +cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j4 --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/gap4' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-2.0.0+b11/tracediff' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/mutscan' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./tracediff -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp +g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 -/usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c +g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[2]: Leaving directory '/build/staden-2.0.0+b11/tracediff' -cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan all -make[2]: Entering directory '/build/staden-2.0.0+b11/mutscan' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp -g++ -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./mutscan -I/build/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c g++ -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm /usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c +/usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 +make[2]: Leaving directory '/build/staden-2.0.0+b11/tracediff' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 make[2]: Leaving directory '/build/staden-2.0.0+b11/mutscan' +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 +gap_range.c: In function 'gap_range_x': +gap_range.c:310:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 310 | if (!HashTableSearch(lib_recs, (char *)r->library_rec, + | ^ +template_display.c: In function 'configure_template': +template_display.c:374:41: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 374 | HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); + | ^ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o preass.o -c preass.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list.o -c list.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probe.o -c probe.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template.o -c template.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 -template_display.c: In function 'configure_template': -template_display.c:374:41: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 374 | HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); - | ^ -gap_range.c: In function 'gap_range_x': -gap_range.c:310:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 310 | if (!HashTableSearch(lib_recs, (char *)r->library_rec, - | ^ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 +find_oligo.c: In function 'StringMatch': +find_oligo.c:957:40: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); + | ^~~ +find_oligo.c:957:41: note: format string is defined here + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); +find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); + | ^~~ +In file included from /usr/include/stdio.h:906, + from /build/staden-2.0.0+b11/./gap5/hache_table.h:5, + from /build/staden-2.0.0+b11/./gap5/g-struct.h:24, + from /build/staden-2.0.0+b11/./gap5/g.h:1, + from tg_struct.h:4, + from tg_gio.h:4, + from io_utils.h:6, + from find_oligo.c:4: +In function 'sprintf', + inlined from 'StringMatch' at find_oligo.c:957:4: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +find_oligo.c: In function 'StringMatch': +find_oligo.c:957:40: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); + | ^~~ +find_oligo.c:957:41: note: format string is defined here + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); +find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] + 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); + | ^~~ +In function 'sprintf', + inlined from 'StringMatch' at find_oligo.c:957:4: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash.o -c hash.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c template_display.c: In function 'template_callback': template_display.c:2354:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, @@ -1868,16 +1965,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c readpair.c: In function 'readpair_obj_func': readpair.c:175:57: warning: '%s' directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", @@ -1895,72 +1988,33 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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 -find_oligo.c: In function 'StringMatch': -find_oligo.c:957:40: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); - | ^~~ -find_oligo.c:957:41: note: format string is defined here - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); -find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); - | ^~~ -In file included from /usr/include/stdio.h:906, - from /build/staden-2.0.0+b11/./gap5/hache_table.h:5, - from /build/staden-2.0.0+b11/./gap5/g-struct.h:24, - from /build/staden-2.0.0+b11/./gap5/g.h:1, - from tg_struct.h:4, - from tg_gio.h:4, - from io_utils.h:6, - from find_oligo.c:4: -In function 'sprintf', - inlined from 'StringMatch' at find_oligo.c:957:4: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -find_oligo.c: In function 'StringMatch': -find_oligo.c:957:40: warning: '%lld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); - | ^~~ -find_oligo.c:957:41: note: format string is defined here - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); -find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] - 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); - | ^~~ -In function 'sprintf', - inlined from 'StringMatch' at find_oligo.c:957:4: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c copy_db.c: In function 'copy_read_name': copy_db.c:118:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] @@ -1980,13 +2034,41 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c +tman_display.c: In function 'repositionSeq': +tman_display.c:279:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] + 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", + | ^~~~~~~~~~~~~~ +tman_display.c:279:18: note: assuming directive output of 12 bytes + 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, + from /usr/include/tcl8.6/tk-private/generic/tk.h:19, + from tman_display.c:1: +In function 'sprintf', + inlined from 'repositionSeq' at tman_display.c:279:5: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clip.o -c clip.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c 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); @@ -2004,8 +2086,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c consistency_display.c: In function 'consistency_callback': consistency_display.c:883:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 883 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, @@ -2023,84 +2103,41 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c +gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libgap5.so -L/build/staden-2.0.0+b11/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc +/usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': +./gap5/tg_index_common.c:105: warning: the use of `tmpnam' is dangerous, better use `mkstemp' +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+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 +/usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c -tman_display.c: In function 'repositionSeq': -tman_display.c:279:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] - 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", - | ^~~~~~~~~~~~~~ -tman_display.c:279:18: note: assuming directive output of 12 bytes - 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, - from /usr/include/tcl8.6/tk-private/generic/tk.h:19, - from tman_display.c:1: -In function 'sprintf', - inlined from 'repositionSeq' at tman_display.c:279:5: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c +make[2]: Leaving directory '/build/staden-2.0.0+b11/gap5' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o undo.o -c undo.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c -gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap5 -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libgap5.so -L/build/staden-2.0.0+b11/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -/usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': -./gap5/tg_index_common.c:105: warning: the use of `tmpnam' is dangerous, better use `mkstemp' -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c -/usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) -make[2]: Leaving directory '/build/staden-2.0.0+b11/gap5' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", @@ -2121,39 +2158,57 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o join.o -c join.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.c copy_db_main.c: In function 'main': copy_db_main.c:86:9: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+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/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/. -I/build/staden-2.0.0+b11/./mutlib -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libgap.so -L/build/staden-2.0.0+b11/lib gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o IO2.o seqInfo.o parse_ft.o IO3.o io_utils.o io_handle.o gap-tcl.o tk-io-reg.o gap_cli_arg.o gap_globals.o newgap_cmds.o init.o consen.o gap_hash.o qual.o qualIO.o bubbl3.o tagdb.o notedb.o active_tags.o dbcheck.o clones.o extract.o preass.o list.o reactions.o probe.o template.o template_display.o ruler_display.o gap_canvas_box.o hash.o gap_array.o show_relationships.o fij.o hash_lib.o do_fij.o auto_assemble.o dis_readings.o find_repeats.o break_contig.o quality_plot.o readpair.o contig_selector.o complement.o cs-object.o list_proc.o dstrand.o oligo_sel.o primlib.o alter_rel.o restriction_enzymes.o stop_codon.o assemble_direct.o check_assembly.o tagU2.o mess.o find_oligo.o copy_db.o contig_order.o clip.o notes.o consistency_display.o consistency_canvas_box.o confidence_graph.o reading_coverage.o readpair_coverage.o strand_coverage.o find_fragments.o vseqs.o legacy_f2c.o f2c.o shuffle_pads.o auto_break.o tkEditor.o tkEdNames.o tkEdUtils.o edInterface.o edUtils2.o tagU1.o undo.o edExtend.o edCommands.o edMutations.o tagEditor.o searchUtils.o tman_interface.o tman_display.o tman_cons.o tman_diff.o contigEditor.o join.o oligo.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz make[2]: Leaving directory '/build/staden-2.0.0+b11/gap4' -cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j3 --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 -j3 --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 -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all -make[2]: Entering directory '/build/staden-2.0.0+b11/prefinish' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo all +cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all make[2]: Entering directory '/build/staden-2.0.0+b11/haplo' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all +make[2]: Entering directory '/build/staden-2.0.0+b11/prefinish' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j4 --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/copy_reads' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 +make[2]: warning: -j4 forced in submake: resetting jobserver mode. +make[2]: Entering directory '/build/staden-2.0.0+b11/convert' +make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish.o -c finish.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c +main.c: In function 'get_db': +main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 87 | fgets(name, sizeof(IOString), stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 92 | fgets(version, sizeof(IOString), stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c 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)); @@ -2169,7 +2224,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c copy_reads.c: In function 'copy_reads': copy_reads.c:409:34: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); @@ -2183,45 +2237,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o process.o -c process.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c +gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./copy_reads -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c +gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz +/usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-2.0.0+b11/copy_reads' -cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert all -make[2]: Entering directory '/build/staden-2.0.0+b11/convert' -make[2]: warning: -j3 forced in submake: resetting jobserver mode. gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./haplo -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c -make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' -main.c: In function 'get_db': -main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 87 | fgets(name, sizeof(IOString), stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 92 | fgets(version, sizeof(IOString), stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./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 +make[2]: Leaving directory '/build/staden-2.0.0+b11/convert' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+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 +make[2]: Leaving directory '/build/staden-2.0.0+b11/haplo' gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c -gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./convert -I/build/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c gcc -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.c -gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -/usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -shared -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -ffile-prefix-map=/build/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b11/./prefinish -I/build/staden-2.0.0+b11/./Misc -I/build/staden-2.0.0+b11/./gap4 -I/build/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-2.0.0+b11/./tk_utils -I/build/staden-2.0.0+b11/./seq_utils -I/build/staden-2.0.0+b11/./primer3/src -I/build/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b11/lib/libprefinish.so finish.o finish_hash.o finish_long.o finish_main.o finish_utils.o finish_walk.o finish_reverse.o finish_filter.o finish_pcr.o dust.o -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 -make[2]: Leaving directory '/build/staden-2.0.0+b11/convert' gcc -L/build/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/arm-linux-gnueabihf -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-2.0.0+b11/prefinish' @@ -2235,7 +2271,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/staden-2.0.0+b11' dh_auto_install - make -j3 install DESTDIR=/build/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/staden-2.0.0+b11' mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden mkdir -p /build/staden-2.0.0+b11/debian/tmp/usr/bin @@ -2249,265 +2285,265 @@ cp ./staden.profile /build/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/staden-2.0.0+b11' -cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./Misc SUBDIR=Misc install -cd trev && make -f /build/staden-2.0.0+b11/./trev/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./trev SUBDIR=trev install -cd primer3 && make -f /build/staden-2.0.0+b11/./primer3/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install +cd Misc && make -f /build/staden-2.0.0+b11/./Misc/Makefile -w -j4 --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 -j4 --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 -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install make[4]: Entering directory '/build/staden-2.0.0+b11/Misc' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/trev' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/primer3' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -install trev /build/staden-2.0.0+b11/debian/tmp/usr/bin +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/primer3/src' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libmisc.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +cp /build/staden-2.0.0+b11/lib/libprimer3.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +install trev /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3' -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev +make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' make[4]: Leaving directory '/build/staden-2.0.0+b11/Misc' +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev +cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install cp /build/staden-2.0.0+b11/./trev/trev.tcl /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev -cd primer3/src && make -f /build/staden-2.0.0+b11/./primer3/src/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install -cd pregap4 && make -f /build/staden-2.0.0+b11/./pregap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install +cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install cp /build/staden-2.0.0+b11/./trev/trevrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc -make[4]: Entering directory '/build/staden-2.0.0+b11/primer3/src' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -make[4]: Entering directory '/build/staden-2.0.0+b11/pregap4' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/trev' -cd spin_emboss && make -f /build/staden-2.0.0+b11/./spin_emboss/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install +cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts install +make[4]: Entering directory '/build/staden-2.0.0+b11/pregap4' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j4 --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/scripts' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/data' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. /build/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' -make[4]: Entering directory '/build/staden-2.0.0+b11/spin_emboss' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /build/staden-2.0.0+b11/lib/libprimer3.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden -install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 -make[4]: Leaving directory '/build/staden-2.0.0+b11/primer3/src' /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' -cp /build/staden-2.0.0+b11/./pregap4/*.tcl /build/staden-2.0.0+b11/./pregap4/widget_licence /build/staden-2.0.0+b11/./pregap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 -cd hetins && make -f /build/staden-2.0.0+b11/./hetins/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins install -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss -make[4]: Entering directory '/build/staden-2.0.0+b11/hetins' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /build/staden-2.0.0+b11/./spin_emboss/*.tcl /build/staden-2.0.0+b11/./spin_emboss/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss -cp /build/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/staden-2.0.0+b11/debian/tmp/usr/bin -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates -cp hetins /build/staden-2.0.0+b11/debian/tmp/usr/bin -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes -cp /build/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl -cp /build/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules -make[4]: Leaving directory '/build/staden-2.0.0+b11/hetins' -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 -cd scripts && make -f /build/staden-2.0.0+b11/./scripts/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./scripts SUBDIR=scripts install -make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' -make[4]: Entering directory '/build/staden-2.0.0+b11/scripts' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cd data && make -f /build/staden-2.0.0+b11/./data/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./data SUBDIR=data install -make[4]: Entering directory '/build/staden-2.0.0+b11/data' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. /build/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' -cp /build/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates +install pregap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 cp /build/staden-2.0.0+b11/./scripts/assemble4 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts +cp /build/staden-2.0.0+b11/./spin_emboss/*.tcl /build/staden-2.0.0+b11/./spin_emboss/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss +cp /build/staden-2.0.0+b11/./pregap4/*.tcl /build/staden-2.0.0+b11/./pregap4/widget_licence /build/staden-2.0.0+b11/./pregap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 /build/staden-2.0.0+b11/./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' -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/./scripts/fasta-split /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/staden-2.0.0+b11/./data/alus/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus -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/./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/pregap4' cp /build/staden-2.0.0+b11/./scripts/staden_help /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts -cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install make[4]: Leaving directory '/build/staden-2.0.0+b11/scripts' -cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install +cp /build/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/staden-2.0.0+b11/debian/tmp/usr/bin +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl +cp /build/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl +cd tk_utils && make -f /build/staden-2.0.0+b11/./tk_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install +cp: 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]: Entering directory '/build/staden-2.0.0+b11/tk_utils' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Leaving directory '/build/staden-2.0.0+b11/spin_emboss' +cd text_utils && make -f /build/staden-2.0.0+b11/./text_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install +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 make[4]: Entering directory '/build/staden-2.0.0+b11/text_utils' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /build/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp /build/staden-2.0.0+b11/lib/libtk_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden -make[4]: Leaving directory '/build/staden-2.0.0+b11/text_utils' mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils -cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi install cp /build/staden-2.0.0+b11/./tk_utils/*.tcl /build/staden-2.0.0+b11/./tk_utils/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils +cp /build/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +make[4]: Leaving directory '/build/staden-2.0.0+b11/text_utils' +cd abi && make -f /build/staden-2.0.0+b11/./abi/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./abi SUBDIR=abi install make[4]: Entering directory '/build/staden-2.0.0+b11/abi' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cp /build/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates cp getABISampleName getABIcomment getABIdate getABIfield /build/staden-2.0.0+b11/debian/tmp/usr/bin -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data -cp /build/staden-2.0.0+b11/./data/blast_data/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data +cp: 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 make[4]: Leaving directory '/build/staden-2.0.0+b11/abi' -cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf install +cd alf && make -f /build/staden-2.0.0+b11/./alf/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./alf SUBDIR=alf install cp /build/staden-2.0.0+b11/./tk_utils/stash /build/staden-2.0.0+b11/debian/tmp/usr/bin -make[4]: Entering directory '/build/staden-2.0.0+b11/alf' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +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 -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 +make[4]: Leaving directory '/build/staden-2.0.0+b11/pregap4' +make[4]: Entering directory '/build/staden-2.0.0+b11/alf' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g install make[4]: Leaving directory '/build/staden-2.0.0+b11/tk_utils' -cd g && make -f /build/staden-2.0.0+b11/./g/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./g SUBDIR=g install -cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data +cp /build/staden-2.0.0+b11/./data/blast_data/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data +cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba install make[4]: Entering directory '/build/staden-2.0.0+b11/g' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cp alfsplit /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/alf' -cp /build/staden-2.0.0+b11/./data/vectors/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors -cd eba && make -f /build/staden-2.0.0+b11/./eba/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./eba SUBDIR=eba install make[4]: Entering directory '/build/staden-2.0.0+b11/eba' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /build/staden-2.0.0+b11/./data/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cp /build/staden-2.0.0+b11/lib/libg.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +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 make[4]: Leaving directory '/build/staden-2.0.0+b11/g' -cp /build/staden-2.0.0+b11/./data/renzyme_bairoch /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc -cd init_exp && make -f /build/staden-2.0.0+b11/./init_exp/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cp eba /build/staden-2.0.0+b11/debian/tmp/usr/bin -make[4]: Entering directory '/build/staden-2.0.0+b11/init_exp' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /build/staden-2.0.0+b11/./data/m13mp18_primers /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/eba' -cp /build/staden-2.0.0+b11/./data/vector_primer /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc -cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field install -cp /build/staden-2.0.0+b11/./data/pam250 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +cd get_scf_field && make -f /build/staden-2.0.0+b11/./get_scf_field/Makefile -w -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./hetins SUBDIR=hetins install make[4]: Entering directory '/build/staden-2.0.0+b11/get_scf_field' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -make[4]: Leaving directory '/build/staden-2.0.0+b11/data' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/hetins' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors cp init_exp /build/staden-2.0.0+b11/debian/tmp/usr/bin -cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install +cp /build/staden-2.0.0+b11/./data/vectors/* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors make[4]: Leaving directory '/build/staden-2.0.0+b11/init_exp' -make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +cd seq_utils && make -f /build/staden-2.0.0+b11/./seq_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install +cp /build/staden-2.0.0+b11/./data/RENZYM.* /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +cp hetins /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/hetins' make[4]: Leaving directory '/build/staden-2.0.0+b11/get_scf_field' +cp /build/staden-2.0.0+b11/./data/renzyme_bairoch /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +make[4]: Entering directory '/build/staden-2.0.0+b11/seq_utils' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +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/./data/vector_primer /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +cp /build/staden-2.0.0+b11/./data/pam250 /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +make[4]: Leaving directory '/build/staden-2.0.0+b11/data' cp /build/staden-2.0.0+b11/lib/libseq_utils.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden cp /build/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-2.0.0+b11/seq_utils' -cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutlib SUBDIR=mutlib install -cd spin && make -f /build/staden-2.0.0+b11/./spin/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./spin SUBDIR=spin install -cd vector_clip && make -f /build/staden-2.0.0+b11/./vector_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install +cd mutlib && make -f /build/staden-2.0.0+b11/./mutlib/Makefile -w -j4 --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 -j4 --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 -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install make[4]: Entering directory '/build/staden-2.0.0+b11/mutlib' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/spin' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/vector_clip' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/screen_seq' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp vector_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libmutlib.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/vector_clip' install spin /build/staden-2.0.0+b11/debian/tmp/usr/bin -cd screen_seq && make -f /build/staden-2.0.0+b11/./screen_seq/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install -make[4]: Leaving directory '/build/staden-2.0.0+b11/mutlib' -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin -make[4]: Entering directory '/build/staden-2.0.0+b11/screen_seq' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip install -cp /build/staden-2.0.0+b11/./spin/*.tcl /build/staden-2.0.0+b11/./spin/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin -make[4]: Entering directory '/build/staden-2.0.0+b11/qclip' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +cd qclip && make -f /build/staden-2.0.0+b11/./qclip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./qclip SUBDIR=qclip install cp screen_seq /build/staden-2.0.0+b11/debian/tmp/usr/bin +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin +make[4]: Leaving directory '/build/staden-2.0.0+b11/mutlib' make[4]: Leaving directory '/build/staden-2.0.0+b11/screen_seq' -cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin -cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install -make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' +make[4]: Entering directory '/build/staden-2.0.0+b11/qclip' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cp /build/staden-2.0.0+b11/./spin/*.tcl /build/staden-2.0.0+b11/./spin/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin +cd polyA_clip && make -f /build/staden-2.0.0+b11/./polyA_clip/Makefile -w -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops install make[4]: Entering directory '/build/staden-2.0.0+b11/polyA_clip' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cd stops && make -f /build/staden-2.0.0+b11/./stops/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./stops SUBDIR=stops install -cp /build/staden-2.0.0+b11/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/stops' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp /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]: warning: -j4 forced in submake: resetting jobserver mode. +cp qclip /build/staden-2.0.0+b11/debian/tmp/usr/bin +make[4]: Leaving directory '/build/staden-2.0.0+b11/qclip' cp polyA_clip /build/staden-2.0.0+b11/debian/tmp/usr/bin -cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin +cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install make[4]: Leaving directory '/build/staden-2.0.0+b11/polyA_clip' -make[4]: Leaving directory '/build/staden-2.0.0+b11/spin' -cd make_weights && make -f /build/staden-2.0.0+b11/./make_weights/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install +cp stops /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/stops' -cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install +cd find_renz && make -f /build/staden-2.0.0+b11/./find_renz/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install make[4]: Entering directory '/build/staden-2.0.0+b11/make_weights' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +cd mutscan && make -f /build/staden-2.0.0+b11/./mutscan/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install make[4]: Entering directory '/build/staden-2.0.0+b11/find_renz' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/mutscan' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp make_weights /build/staden-2.0.0+b11/debian/tmp/usr/bin -cp find_renz /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/make_weights' -cp mutscan /build/staden-2.0.0+b11/debian/tmp/usr/bin +cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install +cp find_renz /build/staden-2.0.0+b11/debian/tmp/usr/bin +make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-2.0.0+b11/find_renz' -cd gap5 && make -f /build/staden-2.0.0+b11/./gap5/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install -cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install +cp mutscan /build/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-2.0.0+b11/mutscan' -make[4]: Entering directory '/build/staden-2.0.0+b11/gap5' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install -make[4]: Entering directory '/build/staden-2.0.0+b11/gap4' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +cd gap4 && make -f /build/staden-2.0.0+b11/./gap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install +cd tracediff && make -f /build/staden-2.0.0+b11/./tracediff/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install make[4]: Entering directory '/build/staden-2.0.0+b11/tracediff' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -cp tracediff /build/staden-2.0.0+b11/debian/tmp/usr/bin -make[4]: Leaving directory '/build/staden-2.0.0+b11/tracediff' +make[4]: Entering directory '/build/staden-2.0.0+b11/gap4' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. install gap5 /build/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 -cp copy_db /build/staden-2.0.0+b11/debian/tmp/usr/bin +cp /build/staden-2.0.0+b11/lib/libspin.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden 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 -install gap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap -cp /build/staden-2.0.0+b11/./gap4/*.tcl /build/staden-2.0.0+b11/./gap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap +cp /build/staden-2.0.0+b11/./spin/*.wts /build/staden-2.0.0+b11/./spin/niprc /build/staden-2.0.0+b11/./spin/siprc /build/staden-2.0.0+b11/./spin/spinrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +cp tracediff /build/staden-2.0.0+b11/debian/tmp/usr/bin +make[4]: Leaving directory '/build/staden-2.0.0+b11/tracediff' +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/./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 copy_db /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/lib/libgap5.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden -cp /build/staden-2.0.0+b11/lib/libgap.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden +install gap4 /build/staden-2.0.0+b11/debian/tmp/usr/bin +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap +cp /build/staden-2.0.0+b11/./gap4/*.tcl /build/staden-2.0.0+b11/./gap4/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp tg_index.bin /build/staden-2.0.0+b11/debian/tmp/usr/bin +install tg_index /build/staden-2.0.0+b11/debian/tmp/usr/bin +install gap5_cmd /build/staden-2.0.0+b11/debian/tmp/usr/bin +make[4]: Leaving directory '/build/staden-2.0.0+b11/gap5' +cp /build/staden-2.0.0+b11/lib/libgap.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden cp /build/staden-2.0.0+b11/./gap4/gaprc /build/staden-2.0.0+b11/./gap4/gaprc_menu_full /build/staden-2.0.0+b11/./gap4/gaprc_menu_mito /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-2.0.0+b11/./gap4/GTAGDB /build/staden-2.0.0+b11/./gap4/NOTEDB /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc -install tg_index /build/staden-2.0.0+b11/debian/tmp/usr/bin 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 -install gap5_cmd /build/staden-2.0.0+b11/debian/tmp/usr/bin 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/gap5' make[4]: Leaving directory '/build/staden-2.0.0+b11/gap4' -cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install -cd haplo && make -f /build/staden-2.0.0+b11/./haplo/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo install -cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install +cd prefinish && make -f /build/staden-2.0.0+b11/./prefinish/Makefile -w -j4 --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 -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./haplo SUBDIR=haplo install +cd copy_reads && make -f /build/staden-2.0.0+b11/./copy_reads/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install +cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert install make[4]: Entering directory '/build/staden-2.0.0+b11/prefinish' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/haplo' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. +make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-2.0.0+b11/copy_reads' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. -mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads +make[4]: warning: -j4 forced in submake: resetting jobserver mode. +make[4]: Entering directory '/build/staden-2.0.0+b11/convert' +make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo -install copy_reads /build/staden-2.0.0+b11/debian/tmp/usr/bin -cp /build/staden-2.0.0+b11/./haplo/*.tcl /build/staden-2.0.0+b11/./haplo/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo cp /build/staden-2.0.0+b11/./prefinish/*.tcl /build/staden-2.0.0+b11/./prefinish/*.itcl /build/staden-2.0.0+b11/./prefinish/*.itk /build/staden-2.0.0+b11/./prefinish/help /build/staden-2.0.0+b11/./prefinish/args.template /build/staden-2.0.0+b11/./prefinish/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish +cp /build/staden-2.0.0+b11/./haplo/*.tcl /build/staden-2.0.0+b11/./haplo/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo +mkdir /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads +install copy_reads /build/staden-2.0.0+b11/debian/tmp/usr/bin +cp staden_convert /build/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/staden-2.0.0+b11/./copy_reads/tclIndex /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads +make[4]: Leaving directory '/build/staden-2.0.0+b11/convert' cp /build/staden-2.0.0+b11/lib/libhaplo.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden -cp /build/staden-2.0.0+b11/lib/libcopy_reads.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden cp /build/staden-2.0.0+b11/./haplo/haplorc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc -cp /build/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc +cp /build/staden-2.0.0+b11/lib/libcopy_reads.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden make[4]: Leaving directory '/build/staden-2.0.0+b11/haplo' -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/./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' -cd convert && make -f /build/staden-2.0.0+b11/./convert/Makefile -w -j3 --jobserver-auth=3,4 BUILD=/build/staden-2.0.0+b11 SRC=/build/staden-2.0.0+b11/./convert SUBDIR=convert install +cp /build/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-2.0.0+b11/lib/libprefinish.so /build/staden-2.0.0+b11/debian/tmp/usr/lib/arm-linux-gnueabihf/staden -make[4]: Entering directory '/build/staden-2.0.0+b11/convert' -make[4]: warning: -j3 forced in submake: resetting jobserver mode. 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 staden_convert /build/staden-2.0.0+b11/debian/tmp/usr/bin -make[4]: Leaving directory '/build/staden-2.0.0+b11/convert' cp /build/staden-2.0.0+b11/./prefinish/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' @@ -2561,8 +2597,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_armhf.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4_armhf.deb'. +dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4_armhf.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-4_all.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-4_armhf.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-4_armhf.changes @@ -2571,12 +2607,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15285/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/6101 and its subdirectories -I: Current time: Wed Jul 12 05:19:38 -12 2023 -I: pbuilder-time-stamp: 1689182378 +I: removing directory /srv/workspace/pbuilder/15285 and its subdirectories +I: Current time: Thu Jul 13 07:44:13 +14 2023 +I: pbuilder-time-stamp: 1689183853