Tue Oct 21 11:24:38 UTC 2025 I: starting to build staden/forky/amd64 on jenkins on '2025-10-21 11:24' Tue Oct 21 11:24:38 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_19/72211/console.log Tue Oct 21 11:24:38 UTC 2025 I: Downloading source for forky/staden=2.0.0+b11-7 --2025-10-21 11:24:39-- http://deb.debian.org/debian/pool/main/s/staden/staden_2.0.0%2bb11-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2403 (2.3K) [text/prs.lines.tag] Saving to: ‘staden_2.0.0+b11-7.dsc’ 0K .. 100% 289M=0s 2025-10-21 11:24:39 (289 MB/s) - ‘staden_2.0.0+b11-7.dsc’ saved [2403/2403] Tue Oct 21 11:24:39 UTC 2025 I: staden_2.0.0+b11-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: staden Binary: staden, staden-common Architecture: any all Version: 2.0.0+b11-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sourceforge.net/projects/staden/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/staden Vcs-Git: https://salsa.debian.org/med-team/staden.git Testsuite: autopkgtest Testsuite-Triggers: procps, xauth, xvfb Build-Depends: debhelper-compat (= 13), libstaden-read-dev, itcl3-dev, itk3-dev, zlib1g-dev, libbz2-dev, liblzma-dev, tcl-dev, tk-dev, tklib, libpng-dev, libncurses-dev, iwidgets4, libcurl4-gnutls-dev Package-List: staden deb science optional arch=any staden-common deb science optional arch=all Checksums-Sha1: a51f0a004961511734a05fd54d8b2b1b0cfd6e32 4754651 staden_2.0.0+b11.orig.tar.gz a2bcf393a941bb0818a9925e61befcac37695b4f 18032 staden_2.0.0+b11-7.debian.tar.xz Checksums-Sha256: cd7ee17626c25bc845ebd3f6311b5a538815fb73a0dfef2393001bf579ac9649 4754651 staden_2.0.0+b11.orig.tar.gz 561471596706f901760ac9e8effda8a4fe721dae89d12f50e20e241cf09a6c6d 18032 staden_2.0.0+b11-7.debian.tar.xz Files: ae59565ded12242c4c2728fbf2e185a7 4754651 staden_2.0.0+b11.orig.tar.gz f4f6c45121d1cf7da4bd13c86d27adf3 18032 staden_2.0.0+b11-7.debian.tar.xz Dgit: 82946ab3913f47bfd5c73955086e7a9dcc15f13a debian archive/debian/2.0.0+b11-7 https://git.dgit.debian.org/staden -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmjS/ioUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpoEA//b5mtrbdrCcNx8AQ08ApilnQdiole H7cIZZGwrIuppnLjwk3ZM2SxMaM9NCvt5T2zALJ5Id4YcCh/ptpAcUQDa0MiK4uv aUOwv2xKPy3bmjpDl9vuYBJd+j+VPdl4FR4aPH6Ai7J1u0qTBnPLYpjOT9vN1Ie8 v325uoqlbBYo1HUe4ui+GwPh0/taA4xauvBl8EMcxQDb8X8vvlxyPpY74X1jlErE NcnMwCrcvBGZ5kZckNsFujhZyORfhqHb9GuQm9D8itpYDE4SeyI+UjiUj61G7x7c hueYCzKtXjpdxVa/d+IlvPUceAfQL/QodP52TeMfzmyOYqgxw0LLvLrzZmC+fLR8 DREAxbbI0M4EtTySp0Hs6iLtcAxbd8QAiY0Dq1XnjJYiRtvOumnO39ALZykSdHg3 MAWmPIOG0bJpKkL/MyxjHa5ZyB66CLReG4Ti+1g/crq5QcTKwS1kYXmJ1WEU3Uf9 qnKksCXVylmjKNu69Xk4VNUzKwObqWrIMpFEGpURzwzr/l8R2hCwPqXLxql5Toqj DIiVb+MBsfOQuHG+0/WAMrIXPjuDlFnA7QZGJDwkDFMvUHsLBtpLLauK9dIMrv/t LfU/DS5pelXI2HXcgwseic5fPaKpRu6YEHJ3WlBtjK56vZXvGsXrWnbtKuj2hSZA UU8r7eZdKir+nm4= =jUuw -----END PGP SIGNATURE----- Tue Oct 21 11:24:39 UTC 2025 I: Checking whether the package is not for us Tue Oct 21 11:24:39 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Oct 21 11:24:39 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Oct 21 11:30:06 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 20 23:24:40 -12 2025 I: pbuilder-time-stamp: 1761045880 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [staden_2.0.0+b11-7.dsc] I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden_2.0.0+b11-7.dsc: no acceptable signature found dpkg-source: info: extracting staden in staden-2.0.0+b11 dpkg-source: info: unpacking staden_2.0.0+b11.orig.tar.gz dpkg-source: info: unpacking staden_2.0.0+b11-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying make_help_menus_work.patch dpkg-source: info: applying fix_tcl_path.patch dpkg-source: info: applying fix_awk.patch dpkg-source: info: applying enable_setting_stadenroot.patch dpkg-source: info: applying include_xalloc.patch dpkg-source: info: applying use_mkstemp_instead_of_tmpnam.patch dpkg-source: info: applying fix_implicit_declaration.patch dpkg-source: info: applying autoconfig.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/724335/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6096bb15d20144ff8c38db60c6a3aedb' 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='724335' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/pbuilderrc_CGOb --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/b1 --logfile b1/build.log staden_2.0.0+b11-7.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/724335/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libstaden-read-dev, itcl3-dev, itk3-dev, zlib1g-dev, libbz2-dev, liblzma-dev, tcl-dev, tk-dev, tklib, libpng-dev, libncurses-dev, iwidgets4, libcurl4-gnutls-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev; however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on itcl3-dev; however: Package itcl3-dev is not installed. pbuilder-satisfydepends-dummy depends on itk3-dev; however: Package itk3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on tcl-dev; however: Package tcl-dev is not installed. pbuilder-satisfydepends-dummy depends on tk-dev; however: Package tk-dev is not installed. pbuilder-satisfydepends-dummy depends on tklib; however: Package tklib is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on iwidgets4; however: Package iwidgets4 is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} itcl3{a} itcl3-dev{a} itk3{a} itk3-dev{a} iwidgets4{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstaden-read-dev{a} libstaden-read14t64{a} libtasn1-6{a} libtasn1-6-dev{a} libtcl8.6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft-dev{a} libxft2{a} libxml2-16{a} libxrender-dev{a} libxrender1{a} libxss-dev{a} libxss1{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tcl{a} tcl-dev{a} tcl8.6{a} tcl8.6-dev{a} tk{a} tk-dev{a} tk8.6{a} tk8.6-dev{a} tklib{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules libtasn1-doc lynx publicsuffix tcllib wget 0 packages upgraded, 146 newly installed, 0 to remove and 0 not upgraded. Need to get 47.7 MB of archives. After unpacking 163 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 26 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 itcl3 amd64 3.4.4-3 [48.2 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 tcl8.6 amd64 8.6.17+dfsg-1 [121 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 tcl8.6-dev amd64 8.6.17+dfsg-1 [1029 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 tcl amd64 8.6.16 [4096 B] Get: 43 http://deb.debian.org/debian forky/main amd64 tcl-dev amd64 8.6.16 [6636 B] Get: 44 http://deb.debian.org/debian forky/main amd64 itcl3-dev amd64 3.4.4-3 [15.5 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 itk3 amd64 3.4.2-5 [26.4 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 64 http://deb.debian.org/debian forky/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 xtrans-dev all 1.6.0-1 [93.5 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libx11-dev amd64 2:1.8.12-1 [894 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libxss-dev amd64 1:1.2.3-1+b3 [22.7 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libpng-dev amd64 1.6.50-1 [366 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 uuid-dev amd64 2.41.2-1 [49.3 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libfontconfig-dev amd64 2.15.0-2.4 [426 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libfontconfig1-dev amd64 2.15.0-2.4 [269 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libxrender-dev amd64 1:0.9.12-1 [39.0 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libxft-dev amd64 2.3.6-1+b4 [73.2 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 tk8.6 amd64 8.6.17-1 [69.7 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 tk8.6-dev amd64 8.6.17-1 [792 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 tk amd64 8.6.16 [4136 B] Get: 87 http://deb.debian.org/debian forky/main amd64 tk-dev amd64 8.6.16 [3968 B] Get: 88 http://deb.debian.org/debian forky/main amd64 itk3-dev amd64 3.4.2-5 [5532 B] Get: 89 http://deb.debian.org/debian forky/main amd64 iwidgets4 all 4.1.1-4 [194 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 93 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.16.0-4 [400 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.24.0-2 [614 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 121 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.9-2 [220 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.2-1 [1322 kB] Get: 126 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 128 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 130 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.12.0-1 [95.5 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.16.0-1 [25.2 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libngtcp2-dev amd64 1.16.0-1 [193 kB] Get: 133 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 134 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 135 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.4-1 [2980 kB] Get: 136 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-2 [375 kB] Get: 138 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls-dev amd64 8.16.0-4 [522 kB] Get: 139 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 140 http://deb.debian.org/debian forky/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get: 142 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 143 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 144 http://deb.debian.org/debian forky/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get: 145 http://deb.debian.org/debian forky/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB] Get: 146 http://deb.debian.org/debian forky/main amd64 tklib all 0.9-1 [1749 kB] Fetched 47.7 MB in 1s (43.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19898 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package tzdata. Preparing to unpack .../001-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../004-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.41.2-1_amd64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.20-2_amd64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../017-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../018-comerr-dev_2.1-1.47.2-3+b3_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../025-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../027-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../028-libxml2-16_2.14.6+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../033-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../034-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../035-fontconfig-config_2.15.0-2.4_amd64.deb ... Unpacking fontconfig-config (2.15.0-2.4) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../036-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... Selecting previously unselected package itcl3:amd64. Preparing to unpack .../037-itcl3_3.4.4-3_amd64.deb ... Unpacking itcl3:amd64 (3.4.4-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../038-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../039-tcl8.6_8.6.17+dfsg-1_amd64.deb ... Unpacking tcl8.6 (8.6.17+dfsg-1) ... Selecting previously unselected package tcl8.6-dev:amd64. Preparing to unpack .../040-tcl8.6-dev_8.6.17+dfsg-1_amd64.deb ... Unpacking tcl8.6-dev:amd64 (8.6.17+dfsg-1) ... Selecting previously unselected package tcl. Preparing to unpack .../041-tcl_8.6.16_amd64.deb ... Unpacking tcl (8.6.16) ... Selecting previously unselected package tcl-dev:amd64. Preparing to unpack .../042-tcl-dev_8.6.16_amd64.deb ... Unpacking tcl-dev:amd64 (8.6.16) ... Selecting previously unselected package itcl3-dev:amd64. Preparing to unpack .../043-itcl3-dev_3.4.4-3_amd64.deb ... Unpacking itcl3-dev:amd64 (3.4.4-3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../044-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../045-libpng16-16t64_1.6.50-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.50-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../046-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../047-libfontconfig1_2.15.0-2.4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2.4) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../048-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../049-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../050-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../051-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../052-libx11-6_2%3a1.8.12-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.12-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../053-libxrender1_1%3a0.9.12-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.12-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../054-libxft2_2.3.6-1+b4_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b4) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../055-libxext6_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package x11-common. Preparing to unpack .../056-x11-common_1%3a7.7+25_all.deb ... 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Setting up bsdextrautils (2.41.2-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 21 11:29:14 UTC 2025. Universal Time is now: Tue Oct 21 11:29:14 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libhtscodecs-dev:amd64 (1.6.1-2) ... Setting up xtrans-dev (1.6.0-1) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.24.0-2) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up libexpat1-dev:amd64 (2.7.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up uuid-dev:amd64 (2.41.2-1) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.5.4-1) ... Setting up libpng16-16t64:amd64 (1.6.50-1) ... Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libnghttp3-dev:amd64 (1.12.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up tcl8.6 (8.6.17+dfsg-1) ... Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up nettle-dev:amd64 (3.10.2-1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up tcl8.6-dev:amd64 (8.6.17+dfsg-1) ... Setting up libpng-dev:amd64 (1.6.50-1) ... Setting up itcl3:amd64 (3.4.4-3) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.16.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.9-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up tcl (8.6.16) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libp11-kit-dev:amd64 (0.25.9-2) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up itcl3-dev:amd64 (3.4.4-3) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.12-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up itk3:amd64 (3.4.2-5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up iwidgets4 (4.1.1-4) ... Setting up tcl-dev:amd64 (8.6.16) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxrender-dev:amd64 (1:0.9.12-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up tk8.6 (8.6.17-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libfontconfig-dev:amd64 (2.15.0-2.4) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-4) ... Setting up debhelper (13.28) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.16.0-1) ... Setting up libxss-dev:amd64 (1:1.2.3-1+b3) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up tk (8.6.16) ... Setting up libxft-dev:amd64 (2.3.6-1+b4) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libfontconfig1-dev:amd64 (2.15.0-2.4) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up tklib (0.9-1) ... Setting up tk8.6-dev:amd64 (8.6.17-1) ... Setting up itk3-dev:amd64 (3.4.2-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.16.0-4) ... Setting up tk-dev:amd64 (8.6.16) ... Setting up libstaden-read-dev (1.15.0-1.1+b2) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/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+b11-7_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' make spotless || true make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' make[2]: *** No rule to make target 'spotless'. Stop. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' rm -f config.log config.status rm -f Makefile shlib.conf staden_config.h system.mk find -name debian -prune -o -name .dir -exec rm '{}' ';' make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:32: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:32: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/libcurl_check_config.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.in:32: the top level configure.in:33: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:33: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_zlib.m4:32: AX_LIB_ZLIB is expanded from... configure.in:33: the top level configure.in:34: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:34: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_lzma.m4:32: AX_LIB_LZMA is expanded from... configure.in:34: the top level configure.in:35: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:35: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_png.m4:34: AX_LIB_PNG is expanded from... configure.in:35: the top level configure.in:40: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:40: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_staden_io_lib.m4:35: AX_LIB_IO_LIB is expanded from... configure.in:40: the top level configure.in:43: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:43: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_curses.m4:37: AX_LIB_CURSES is expanded from... configure.in:43: the top level configure.in:46: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:46: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:46: the top level configure.in:93: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:43: TEA_PATH_TCLCONFIG is expanded from... configure.in:93: the top level configure.in:94: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:94: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:355: TEA_LOAD_TCLCONFIG is expanded from... configure.in:94: the top level configure.in:96: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:96: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:200: TEA_PATH_TKCONFIG is expanded from... configure.in:96: the top level configure.in:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:2704: TEA_TCL_EARLY_FLAG is expanded from... ac_stubs/tcl.m4:2717: TEA_TCL_EARLY_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:148: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:148: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_tklib.m4:27: AX_LIB_TKLIB is expanded from... configure.in:148: the top level configure.in:149: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:149: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_iwidgets.m4:28: AX_LIB_IWIDGETS is expanded from... configure.in:149: the top level configure.in:150: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:150: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itcl.m4:26: AX_LIB_ITCL is expanded from... configure.in:150: the top level configure.in:151: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:151: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itk.m4:26: AX_LIB_ITK is expanded from... configure.in:151: the top level autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_configure -- --enable-64bit \ --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu \ --with-itk=/usr/lib/tcltk/x86_64-linux-gnu ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-64bit --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu --with-itk=/usr/lib/tcltk/x86_64-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 8.16.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking for png.h... yes checking for staden-io_lib-config... no checking for io_lib-config... /usr/bin/io_lib-config checking if io_lib version >= 1.12.5... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking for ncurses.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes checking for pwd.h... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for declarations of fseeko and ftello... yes checking for library containing cos... -lm checking for popen... yes checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... no checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking for egrep -e... (cached) /usr/bin/grep -E checking if 64bit support is requested... yes 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-6.12.48+deb13-amd64 checking for ar... ar checking if compiler accepts -m64 flag... yes checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... using long checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include/tcl8.6 checking for Tcl private include files... Using srcdir found in tclConfig.sh: /usr/include/tcl8.6/tcl-private checking for Tk public headers... /usr/include/tcl8.6 checking for Tk private include files... Using srcdir found in tkConfig.sh: /usr/include/tcl8.6/tk-private checking tklib directory... yes (/usr/share/tcltk/tklib0.9) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/x86_64-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/x86_64-linux-gnu/itk3.4) configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/share/tcltk/tklib0.9 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/x86_64-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/x86_64-linux-gnu/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' cd Misc && make -f /build/reproducible-path/staden-2.0.0+b11/./Misc/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./Misc SUBDIR=Misc all cd primer3 && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src all cd trev && make -f /build/reproducible-path/staden-2.0.0+b11/./trev/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./trev SUBDIR=trev all cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[2]: warning: -j40 forced in submake: resetting jobserver mode. /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o crash.o -c crash.c /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o date.o -c date.c make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o -c dpal.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shell.o -c shell.c Nothing to build for scripts. Nothing to build for Pregap4. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c Nothing to build for spin_emboss. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' /build/reproducible-path/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o boulder_input.o -c boulder_input.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c mkdir -p /build/reproducible-path/staden-2.0.0+b11/lib 2>/dev/null gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o error.o -c error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c Nothing to build for data. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' touch /build/reproducible-path/staden-2.0.0+b11/lib/.dir gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array.o -c array.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o locks.o -c locks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c: In function 'boulder_print_oligos': primer3_main.c:416:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 416 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:416:30: note: directive argument in the range [1, 2147483647] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:970, from primer3_main.c:7: In function 'sprintf', inlined from 'boulder_print_oligos' at primer3_main.c:416:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ parse_db.c: In function 'parse_entry': parse_db.c:234:66: warning: '%s' directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); | ^~ ~~~~ In file included from /usr/include/stdio.h:970, from parse_db.c:19: In function 'sprintf', inlined from 'parse_entry' at parse_db.c:234:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 33 and 8224 bytes into a destination of size 8192 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ primer3_main.c: In function 'main': primer3_main.c:234:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); | ^~ In function 'boulder_print_pairs', inlined from 'main' at primer3_main.c:109:3: primer3_main.c:234:30: note: directive argument in the range [1, 2147483646] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In function 'sprintf', inlined from 'boulder_print_pairs' at primer3_main.c:234:7, inlined from 'main' at primer3_main.c:109:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/Misc' cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi all cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g all cd alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./alf SUBDIR=alf all cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/abi' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/g' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[2]: warning: -j40 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o cli_arg.o -c cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tclXkeylist.o -c tclXkeylist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tclXutil.o -c tclXutil.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./alf -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./init_exp -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_debug.o -c tcl_debug.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./hetins -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o misc.o -c misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./eba -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./get_scf_field -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o text_output.o -c text_output.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./eba -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkRaster.o -c tkRaster.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o sheet.o -c sheet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkSheet.o -c tkSheet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkSheet_common.o -c tkSheet_common.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o trace_print.o -c trace_print.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o postscript.o -c postscript.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o split.o -c split.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTrace.o -c tkTrace.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceComp.o -c tkTraceComp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceIO.o -c tkTraceIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceDisp.o -c tkTraceDisp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o capture.o -c capture.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o canvas_box.o -c canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o ruler_tick.o -c ruler_tick.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o restriction_enzyme_map.o -c restriction_enzyme_map.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o element_canvas.o -c element_canvas.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o container.o -c container.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o container_ruler.o -c container_ruler.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_io_lib.o -c tcl_io_lib.c alfsplit.c: In function 'main': alfsplit.c:347:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 363 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function 'readIndexEntry': alfsplit.c:129:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | fread (ent->label,40,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:135:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 135 | fread (junk,70,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm capture.c: In function 'tcl_capture': capture.c:53:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | read(fd, buf, statbuf.st_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/reproducible-path/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 In file included from tkRaster.c:45: tkRaster.c: In function 'DrawEnvIndex': tkRaster.c:2266:62: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2266 | entryPtr = Tcl_FindHashEntry (&(RasterPtr->drawEnvTable), (char*)drawenvno); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ tkRaster.c: In function 'CreateDrawEnv': tkRaster.c:2353:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2353 | (char*) (RasterPtr->drawEnvCount), | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ tkRaster.c: In function 'DestroyDrawEnv': tkRaster.c:2381:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2381 | (char*)(drawenvptr->index)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ 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]) ; | ^~ In file included from /usr/include/stdio.h:970, from alfsplit.c:30: In function 'sprintf', inlined from 'main' at alfsplit.c:312:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 2563 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ tkTraceDisp.c: In function 'trace_draw_numbers': tkTraceDisp.c:746:32: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 746 | sprintf(number, "%d", cind); | ^ In file included from /usr/include/stdio.h:970, from tkTraceDisp.c:2: In function 'sprintf', inlined from 'trace_draw_numbers' at tkTraceDisp.c:746:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' gcc -L/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/alf' gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/reproducible-path/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/reproducible-path/staden-2.0.0+b11/primer3/src' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' make[2]: warning: -j40 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss2.o -c align_ss2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_sv.o -c align_sv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dna_utils.o -c dna_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib.o -c align_lib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.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); | ^~~~~~~~~~~~~~~~~~~~~~~~ renz_utils.c: In function 'SetREnzColour': renz_utils.c:1049:35: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 1049 | sprintf(colour, "#%02x%02x%02x", r, g, b); | ^ In file included from /usr/include/stdio.h:970, from renz_utils.c:3: In function 'sprintf', inlined from 'SetREnzColour' at renz_utils.c:1049:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 26 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin all cd vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip all cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./qclip SUBDIR=qclip all cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[2]: warning: -j40 forced in submake: resetting jobserver mode. cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap5 SUBDIR=gap5 all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[2]: warning: -j40 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./vector_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o qclip.o -c qclip.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./screen_seq -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./stops -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedUtils.o -c tkSeqedUtils.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqedInterface.o -c seqedInterface.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpam.o -c readpam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_similar_spans.o -c sip_similar_spans.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_globals.o -c sip_globals.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_cache.o -c tracealign_cache.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probs.o -c probs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sim.o -c sim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./make_weights -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./find_renz -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c seq_reg_cmds.c: In function 'GetActiveSeqName': raster_cmds.c: In function 'RasterResults': raster_cmds.c:250:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 250 | zoom = (int)gen.result; | ^ seq_reg_cmds.c:919:32: warning: zero-length gnu_printf format string [-Wformat-zero-length] 919 | vTcl_SetResult(interp, ""); | ^~ seq_raster.c: In function 'GetRasterZoom': seq_raster.c:1512:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1512 | result = (int)gen.result; | ^ sip_align.c: In function 'align_callback': sip_align.c:181:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 181 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c seq_raster.c: In function 'seq_raster_callback': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c seq_raster.c:3012:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3012 | jdata->info.result = (void *)zoom; | ^ seq_raster.c:3034:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3034 | jdata->info.result = (void *)zoom; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c nip_gene_search.c: In function 'plot_gene_search_callback': nip_gene_search.c:206:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 206 | jdata->info.result = (void *)id; | ^ sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:316:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 316 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from /build/reproducible-path/staden-2.0.0+b11/./tk_utils/tkRaster.h:9, from seq_reg.h:6, from sequence_pair_display.c:4: In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:316:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:344:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 344 | sprintf(tmp, "%10d", i*10); | ^ In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:344:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sip_similar_spans.c: In function 'similar_spans_callback': sip_similar_spans.c:289:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 289 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c sip_find_identity.c: In function 'identities_callback': sip_find_identity.c:210:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 210 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c nip_stop_codon.c: In function 'nip_stop_codons_callback': nip_stop_codon.c:195:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 195 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c sip_quick_scan.c: In function 'quick_scan_callback': sip_quick_scan.c:234:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 234 | jdata->info.result = (void *)id; | ^ emboss_input_funcs.c: In function 'emboss_graph_callback': emboss_input_funcs.c:260:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 260 | jdata->info.result = (void *)id; | ^ sip_sim.c: In function 'sim_callback': sip_sim.c:197:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 197 | jdata->info.result = (void *)id; | ^ gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -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': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c 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 -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm sp_hash_lib.cpp: In function 'int sp::hash_word8n(char*, int*, int, int, short unsigned int*)': sp_hash_lib.cpp:57:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 57 | register int i; | ^ sp_hash_lib.cpp:58:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:58:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:58:38: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:59:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 59 | register int unsigned short luword; | ^~~~~~ sp_hash_lib.cpp: In function 'int sp::hash_seq8n(char*, int*, int, int)': sp_hash_lib.cpp:99:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp: In function 'int sp::hash_word4n(char*, int*, int, int, unsigned char*)': sp_hash_lib.cpp:156:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 156 | register int i; | ^ sp_hash_lib.cpp:157:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:157:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:157:38: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:158:28: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 158 | register char unsigned luword; | ^~~~~~ sp_hash_lib.cpp: In function 'int sp::hash_seq4n(char*, int*, int, int)': sp_hash_lib.cpp:197:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp:197:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ nip_trna_search.c: In function 'trna_search_callback': nip_trna_search.c:173:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 173 | jdata->info.result = (void *)id; | ^ sp_hash_lib.cpp:197:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp: In function 'void sp::remdup(int*, int*, int*, int*)': sp_hash_lib.cpp:411:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 411 | register int i; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c nip_base_comp.c: In function 'plot_base_comp_callback': nip_base_comp.c:183:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c nip_splice_search.c: In function 'splice_search_callback': nip_splice_search.c:183:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/stops' nip_string_search.c: In function 'nip_string_search_callback': nip_string_search.c:170:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 170 | jdata->info.result = (void *)id; | ^ nip_wtmatrix_search.c: In function 'nip_wtmatrix_search_callback': nip_wtmatrix_search.c:167:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 167 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c find_oligo.c: In function 'StringMatch': find_oligo.c:957:40: warning: '%ld' 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:970, from /build/reproducible-path/staden-2.0.0+b11/./gap5/hache_table.h:5, from /build/reproducible-path/staden-2.0.0+b11/./gap5/g-struct.h:24, from /build/reproducible-path/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/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.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:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, 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/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' cp /build/reproducible-path/staden-2.0.0+b11/./mutlib/mutlib.def 2>&- make[2]: [/build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile:81: /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libgap5.so -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/./gap5/tg_index_common.c:105:(.text+0x580): warning: the use of `tmpnam' is dangerous, better use `mkstemp' cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutscan SUBDIR=mutscan all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap4' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[2]: warning: -j40 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tracediff -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o preass.o -c preass.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list.o -c list.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probe.o -c probe.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template.o -c template.c io_utils.c: In function 'template_name_to_number': io_utils.c:38:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 38 | return (int)Tcl_GetHashValue(hash); | ^ io_utils.c: In function 'read_name_to_number': io_utils.c:84:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 84 | return (int)Tcl_GetHashValue(hash); | ^ In file included from IO1.h:50, from io_utils.h:6, from io_utils.c:6: io_utils.c: In function 'cache_template_name': io_utils.c:549:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 549 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2556:64: note: in definition of macro 'Tcl_SetHashValue' 2556 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (void *)(value)) | ^~~~~ io_utils.c: In function 'cache_read_name': io_utils.c:566:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 566 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2556:64: note: in definition of macro 'Tcl_SetHashValue' 2556 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (void *)(value)) | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c actf.c: In function 'actf_lock': actf.c:246:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 246 | write(fd, db_path, strlen(db_path)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash.o -c hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c tk-io-reg.c: In function 'tk_result_is_consistency': tk-io-reg.c:604:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 604 | if (args.cons_id == (int)gen.data) { | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clip.o -c clip.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c readpair.c: In function 'readpair_obj_func': readpair.c:175:57: warning: '%s' directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", | ^~ 176 | *handle, c_list); | ~~~~~~ In file included from /usr/include/stdio.h:970, from readpair.c:18: In function 'sprintf', inlined from 'readpair_obj_func' at readpair.c:175:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 27 and 1060 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c /usr/bin/ld: warning: libtk_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c /usr/bin/ld: warning: libtk_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) copy_db.c: In function 'copy_read_name': copy_db.c:118:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 118 | sprintf(num, "#%d", iter++); | ^~ copy_db.c:118:30: note: directive argument in the range [1, 2147483646] 118 | sprintf(num, "#%d", iter++); | ^~~~~ In file included from /usr/include/stdio.h:970, from copy_db.c:1: In function 'sprintf', inlined from 'copy_read_name' at copy_db.c:118:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c consistency_display.c: In function 'consistency_join': consistency_display.c:160:22: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | gen.data = (void *)remove_dup; | ^ confidence_graph.c: In function 'confidence_callback': confidence_graph.c:531:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 531 | jdata->generic.data = (void *)conf->cons_id; | ^ confidence_graph.c:624:44: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 624 | confidence_join(io, c, conf, (int)jdata->generic.data); | ^ readpair_coverage.c: In function 'readpair_coverage_callback': readpair_coverage.c:500:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 500 | jdata->generic.data = (void *)rcov->cons_id; | ^ reading_coverage.c: In function 'reading_coverage_callback': reading_coverage.c:552:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 552 | jdata->generic.data = (void *)rcov->cons_id; | ^ readpair_coverage.c:594:51: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 594 | readpair_coverage_join(io, c, rcov, (int)jdata->generic.data); | ^ reading_coverage.c:645:50: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 645 | reading_coverage_join(io, c, rcov, (int)jdata->generic.data); | ^ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' In file included from vseqs.c:3: vseqs.c: In function 'new_vcontig': strand_coverage.c: In function 'strand_coverage_callback': strand_coverage.c:503:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 503 | jdata->generic.data = (void *)scov->cons_id; | ^ strand_coverage.c:541:49: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 541 | strand_coverage_join(io, c, scov, (int)jdata->generic.data); | ^ vseqs.c:60:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 60 | hash = Tcl_CreateHashEntry(&db->num_hash, (char *)rnum, | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function 'new_vrseq': vseqs.c:158:51: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 158 | hash = Tcl_CreateHashEntry(&vc->num_hash, (char *)(vrseq->rnum), &new); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function 'del_vrseq': vseqs.c:215:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 215 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)(vrseq->rnum)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ vseqs.c: In function 'vrseq_index2ptr': vseqs.c:409:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 409 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)num); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o undo.o -c undo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c notes.c: In function 'time_t2str': notes.c:829:21: warning: ' (' directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 829 | sprintf(buf, "%s (%ld)", buf2, (long)t); | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from notes.c:11: In function 'sprintf', inlined from 'time_t2str' at notes.c:829:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1047 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o join.o -c join.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.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, | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from consistency_display.c:1: In function 'sprintf', inlined from 'consistency_callback' at consistency_display.c:883:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ copy_db_main.c: In function 'main': copy_db_main.c:86:9: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/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/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: In function 'sprintf', inlined from 'repositionSeq' at tman_display.c:281:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ template_display.c: In function 'template_callback': template_display.c:2354:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from template_display.c:2: In function 'sprintf', inlined from 'template_callback' at template_display.c:2354:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libgap.so -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/reproducible-path/staden-2.0.0+b11/./prefinish/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd haplo && make -f /build/reproducible-path/staden-2.0.0+b11/./haplo/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd copy_reads && make -f /build/reproducible-path/staden-2.0.0+b11/./copy_reads/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo771600 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./convert SUBDIR=convert all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[2]: warning: -j40 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[2]: warning: -j40 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish.o -c finish.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_filter.o -c finish_filter.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o process.o -c process.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.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 -L/build/reproducible-path/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/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/reproducible-path/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/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/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/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) copy_reads.c: In function 'create_si_struct': copy_reads.c:125:26: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 125 | sprintf(comment, "%s %s", tag_text, io_name(io)); | ^~ In file included from /usr/include/stdio.h:970, from copy_reads.c:4: In function 'sprintf', inlined from 'create_si_struct' at copy_reads.c:125:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ copy_reads.c: In function 'copy_reads': copy_reads.c:409:34: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); | ^~ In function 'sprintf', inlined from 'copy_reads' at copy_reads.c:409:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/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/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -L/build/reproducible-path/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/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/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/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu17 -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_install make -j40 install DESTDIR=/build/reproducible-path/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/doc mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/man cp shlib.conf /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp ./staden.profile /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' cd Misc && make -f /build/reproducible-path/staden-2.0.0+b11/./Misc/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./Misc SUBDIR=Misc install cd trev && make -f /build/reproducible-path/staden-2.0.0+b11/./trev/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./trev SUBDIR=trev install cd primer3 && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: warning: -j40 forced in submake: resetting jobserver mode. install trev /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libmisc.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cp /build/reproducible-path/staden-2.0.0+b11/lib/libprimer3.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' install pregap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/Misc' /build/reproducible-path/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss cp /build/reproducible-path/staden-2.0.0+b11/./scripts/assemble4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/reproducible-path/staden-2.0.0+b11/./trev/trev.tcl /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install cp /build/reproducible-path/staden-2.0.0+b11/./trev/trevrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install cp /build/reproducible-path/staden-2.0.0+b11/./scripts/fasta-split /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/*.tcl /build/reproducible-path/staden-2.0.0+b11/./pregap4/widget_licence /build/reproducible-path/staden-2.0.0+b11/./pregap4/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi install cd alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./alf SUBDIR=alf install cp /build/reproducible-path/staden-2.0.0+b11/./data/alus/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/reproducible-path/staden-2.0.0+b11/./scripts/fasta2exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/abi' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba install cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/./scripts/splitseq_da /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/g' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[4]: warning: -j40 forced in submake: resetting jobserver mode. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cp /build/reproducible-path/staden-2.0.0+b11/./scripts/staden_help /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[4]: warning: -j40 forced in submake: resetting jobserver mode. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field install cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins install cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cp: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory cp /build/reproducible-path/staden-2.0.0+b11/lib/libtext_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp alfsplit /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: [/build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:30: install] Error 1 (ignored) cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/emboss_menu /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/spin_embossrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp getABISampleName getABIcomment getABIdate getABIfield /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libtk_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/lib/libg.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp eba /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' cp init_exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cp get_scf_field /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp hetins /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' cp /build/reproducible-path/staden-2.0.0+b11/./data/blast_data/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/*.tcl /build/reproducible-path/staden-2.0.0+b11/./tk_utils/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates cp: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes make[4]: [/build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile:42: install] Error 1 (ignored) cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/naming_schemes/*.p4t /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/reproducible-path/staden-2.0.0+b11/./data/gcodes/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/pregap4rc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/stash /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/2bars_*.bmp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/help_config /build/reproducible-path/staden-2.0.0+b11/./tk_utils/tk_utilsrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors cp /build/reproducible-path/staden-2.0.0+b11/./data/vectors/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install cp /build/reproducible-path/staden-2.0.0+b11/./data/RENZYM.* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/./data/renzyme_bairoch /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./data/m13mp18_primers /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/./data/vector_primer /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./data/pam250 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/reproducible-path/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib install cd spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin install cd vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./qclip SUBDIR=qclip install cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp vector_clip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp screen_seq /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp stops /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp qclip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin install spin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp polyA_clip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' cp make_weights /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin cp find_renz /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install cp /build/reproducible-path/staden-2.0.0+b11/./spin/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap4' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/lib/libspin.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install gap5 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp tracediff /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp mutscan /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./spin/*.wts /build/reproducible-path/staden-2.0.0+b11/./spin/niprc /build/reproducible-path/staden-2.0.0+b11/./spin/siprc /build/reproducible-path/staden-2.0.0+b11/./spin/spinrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' cp /build/reproducible-path/staden-2.0.0+b11/./gap5/*.tcl /build/reproducible-path/staden-2.0.0+b11/./gap5/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' cp /build/reproducible-path/staden-2.0.0+b11/./gap5/../gap4/acd2tag.tcl /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp copy_db /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./gap5/gap5rc /build/reproducible-path/staden-2.0.0+b11/./gap5/gap5rc_menu_full /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc install gap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libgap5.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp /build/reproducible-path/staden-2.0.0+b11/./gap4/*.tcl /build/reproducible-path/staden-2.0.0+b11/./gap4/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp tg_index.bin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libgap.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install tg_index /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin install gap5_cmd /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./gap4/gaprc /build/reproducible-path/staden-2.0.0+b11/./gap4/gaprc_menu_full /build/reproducible-path/staden-2.0.0+b11/./gap4/gaprc_menu_mito /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' cp /build/reproducible-path/staden-2.0.0+b11/./gap4/GTAGDB /build/reproducible-path/staden-2.0.0+b11/./gap4/NOTEDB /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./gap4/cap2rc /build/reproducible-path/staden-2.0.0+b11/./gap4/cap3rc /build/reproducible-path/staden-2.0.0+b11/./gap4/fak2rc /build/reproducible-path/staden-2.0.0+b11/./gap4/phraprc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./gap4/*.bitmap /build/reproducible-path/staden-2.0.0+b11/./gap4/*.gif /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/reproducible-path/staden-2.0.0+b11/./prefinish/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install cd haplo && make -f /build/reproducible-path/staden-2.0.0+b11/./haplo/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./haplo SUBDIR=haplo install cd copy_reads && make -f /build/reproducible-path/staden-2.0.0+b11/./copy_reads/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' make[4]: warning: -j40 forced in submake: resetting jobserver mode. cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -j40 --jobserver-auth=fifo:/tmp/GMfifo777186 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./convert SUBDIR=convert install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[4]: warning: -j40 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[4]: warning: -j40 forced in submake: resetting jobserver mode. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/reproducible-path/staden-2.0.0+b11/./haplo/*.tcl /build/reproducible-path/staden-2.0.0+b11/./haplo/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads cp staden_convert /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.tcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itk /build/reproducible-path/staden-2.0.0+b11/./prefinish/help /build/reproducible-path/staden-2.0.0+b11/./prefinish/args.template /build/reproducible-path/staden-2.0.0+b11/./prefinish/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish install copy_reads /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' cp /build/reproducible-path/staden-2.0.0+b11/lib/libhaplo.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/reproducible-path/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/reproducible-path/staden-2.0.0+b11/./copy_reads/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads cp /build/reproducible-path/staden-2.0.0+b11/./haplo/haplorc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/lib/libcopy_reads.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/config.prefinish /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/haplo' cp /build/reproducible-path/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/lib/libprefinish.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' install prefinish /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_sanger /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_cDNA /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_cDNA_ends_only \ /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/rules/*.rule /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/config.prefinish /build/reproducible-path/staden-2.0.0+b11/./prefinish/prefinishrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' make[3]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' # Remove file causing lintian errors that is targeting at windows find debian -name help_windows.tcl -delete # Remove some empty directories find debian -type d -empty -name acdtcl -delete find debian -type d -empty -name templates -delete # Build system is not prepared for multi-arch mv /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-7_all.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-7_amd64.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-7_amd64.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/724335 and its subdirectories I: Current time: Mon Oct 20 23:30:06 -12 2025 I: pbuilder-time-stamp: 1761046206 Tue Oct 21 11:30:07 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Oct 21 11:30:07 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Oct 21 11:34:47 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Oct 21 11:34:48 UTC 2025 I: staden_2.0.0+b11-7_amd64.changes: Format: 1.8 Date: Tue, 23 Sep 2025 21:54:54 +0200 Source: staden Binary: staden staden-common staden-dbgsym Architecture: all amd64 Version: 2.0.0+b11-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: staden - DNA sequence assembly (Gap4/Gap5), editing and analysis tools staden-common - Architecture independent files for Staden Closes: 1097934 Changes: staden (2.0.0+b11-7) unstable; urgency=medium . * d/rules: fortify sources. * d/control: add myself to uploaders. * d/control: remove redundant Rules-Requires-Root. * d/watch: bump to uscan v5 watch file. * d/u/metadata: fix typoed Bug fields. * d/rules: fix build failure with gcc-15. Thanks to Adrian Bunk (Closes: #1097934) Checksums-Sha1: 62ba1cf76825d33a684cb069f3410db1cf2f76d4 1971144 staden-common_2.0.0+b11-7_all.deb c22622d3a1cb822c3e77c3de22647d8e8da68a9e 4469944 staden-dbgsym_2.0.0+b11-7_amd64.deb 8944e74f92a01fd6642e13d63b1176dccf60aeeb 8670 staden_2.0.0+b11-7_amd64.buildinfo 5fe20516bfd5a2160b1f13a28ea3486c2fb27207 1666540 staden_2.0.0+b11-7_amd64.deb Checksums-Sha256: 3c000162fce54b15b1df2bb2b5430ab0fa8d985efa6ad3bbcb3f08f7ebd4f768 1971144 staden-common_2.0.0+b11-7_all.deb 52a870a44a8f1e05364a0b343e596b65fd0c6038226868f1f4d5ce30208ec59a 4469944 staden-dbgsym_2.0.0+b11-7_amd64.deb 6c058fa8cf61fb31de23b505fb3312820e1b33858ac190fa2e7ea370d9fbe158 8670 staden_2.0.0+b11-7_amd64.buildinfo c075467714ca68305ea5839e9c2156b2e1c95e307d05dfe88a0ce320cd7ad9fe 1666540 staden_2.0.0+b11-7_amd64.deb Files: 7fda27f4d76dd2eddffc096ac31c23ec 1971144 science optional staden-common_2.0.0+b11-7_all.deb a3e9f9fd3a55899d51e6c1ef97ad1d12 4469944 debug optional staden-dbgsym_2.0.0+b11-7_amd64.deb 644adbe05b0cd4619ba25656a085d383 8670 science optional staden_2.0.0+b11-7_amd64.buildinfo dfbf9e999c535710f498153b6c3fdeb2 1666540 science optional staden_2.0.0+b11-7_amd64.deb Tue Oct 21 11:34:48 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_19-72211.service; invocation ID: c9fa82feaf204d75a095d6c4eb84e20e # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/staden_2.0.0+b11-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/staden_2.0.0+b11-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/staden_2.0.0+b11-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/b1/staden_2.0.0+b11-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WQzfIUZg/b2/staden_2.0.0+b11-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 219ms CPU time consumed: 164ms Memory peak: 17.6M (swap: 0B) Tue Oct 21 11:34:49 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 21 11:34:49 UTC 2025 I: staden from forky built successfully and reproducibly on amd64. Tue Oct 21 11:34:50 UTC 2025 I: Removing signed staden_2.0.0+b11-7_amd64.buildinfo.asc files: removed './b1/staden_2.0.0+b11-7_amd64.buildinfo.asc' removed './b2/staden_2.0.0+b11-7_amd64.buildinfo.asc'