Wed Mar 5 11:45:06 UTC 2025 I: starting to build staden/unstable/amd64 on jenkins on '2025-03-05 11:44' Wed Mar 5 11:45:06 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_38/49398/console.log Wed Mar 5 11:45:06 UTC 2025 I: Downloading source for unstable/staden=2.0.0+b11-5 --2025-03-05 11:45:06-- http://deb.debian.org/debian/pool/main/s/staden/staden_2.0.0%2bb11-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2185 (2.1K) [text/prs.lines.tag] Saving to: ‘staden_2.0.0+b11-5.dsc’ 0K .. 100% 304M=0s 2025-03-05 11:45:06 (304 MB/s) - ‘staden_2.0.0+b11-5.dsc’ saved [2185/2185] Wed Mar 5 11:45:06 UTC 2025 I: staden_2.0.0+b11-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: staden Binary: staden, staden-common Architecture: any all Version: 2.0.0+b11-5 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://sourceforge.net/projects/staden/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/staden Vcs-Git: https://salsa.debian.org/med-team/staden.git 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 a770dce5dc8fb2dad9e1e8a8a85ec4be8ef3b8ac 16800 staden_2.0.0+b11-5.debian.tar.xz Checksums-Sha256: cd7ee17626c25bc845ebd3f6311b5a538815fb73a0dfef2393001bf579ac9649 4754651 staden_2.0.0+b11.orig.tar.gz 34008f109d1a4c97659213035fe72c0059d9e4caa80b65d6e972e0055fc32ecf 16800 staden_2.0.0+b11-5.debian.tar.xz Files: ae59565ded12242c4c2728fbf2e185a7 4754651 staden_2.0.0+b11.orig.tar.gz 532a8c853e97a38ddbc4e95e93525f66 16800 staden_2.0.0+b11-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmXxuwcACgkQPCZ2P2xn 5uI/qw//dVWXAscRvuRAcyK8UpglQNEVAJLZJg7DO+832OyOfd84naHsh610D6yP xNL4dOhyV6K+2fm62wF72Hx9AY/vyXRMaiEirnxm4NskiNkXU5lN51hPnyMeEAz+ yTR4K65U7Dw7TchgIZ2YZ5DSk6k2Yxcr3hCSOBmvr9RRm3YuWVMelCo1uuPyTlCj S4NZ2wY+afWXvp4vDb0KUed8BeuX1XEomACWUJpXG8W6d5ZULPXN9ShRCuuDczoL aQ3IQC+TeKSU03x6jnJEyyEpRcUBv7F/+rauAQ+TGZGKqcc5746UkHhQQQaGi4aa QTU9z66CoQ/EQysdx+oMXJYgiepwIdjRhmINeOD25c62oAMktmRzgQZs3O+YYuEo ao/HxNR3/o1DACvXbM47Qhe7OSsz/hlBFIiiuLQm9/3Kz6NXnxbN/dKbBA1MZawZ Cijb6yOPJu4b0UqTv8khNnCK2EEM0pztLM61ntOhgS1VJfi2xzMDPAMJ/Vie7QRV snwTGa+vGINPhVMsCwXPzUeXz4/Dj52j3JV5Ty8dP65tuF/Po9OjTRkMDklFyGcz a0Gw/jsCAwqPVwvpli1b4jwGe0NqROF7SmLY+35+FBc3glZC2TShD6QzfYiXgNWY zFtUxsljJhcCD1htF4+6TIO2D8v7fijtaFRPlXkCbI3Wl9zBpNg= =Q0m3 -----END PGP SIGNATURE----- Wed Mar 5 11:45:06 UTC 2025 I: Checking whether the package is not for us Wed Mar 5 11:45:06 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Wed Mar 5 11:45:06 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Wed Mar 5 11:46:55 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 7 06:08:09 -12 2026 I: pbuilder-time-stamp: 1775585289 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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+b11-5.dsc] I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden_2.0.0+b11-5.dsc: unsupported subcommand 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+b11-5.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2429740/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=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e528f93edcde4ecc9aa9397817037f32' 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='2429740' 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.wlj8N73S/pbuilderrc_UThc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/b1 --logfile b1/build.log staden_2.0.0+b11-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2429740/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 ... 19783 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} libicu72{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{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, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 56.6 MB of archives. After unpacking 195 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 itcl3 amd64 3.4.4-2.1 [48.1 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 itk3 amd64 3.4.2-4 [26.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 tcl8.6 amd64 8.6.16+dfsg-1 [121 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 tcl8.6-dev amd64 8.6.16+dfsg-1 [1032 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 tcl amd64 8.6.14 [4032 B] Get: 60 http://deb.debian.org/debian unstable/main amd64 tcl-dev amd64 8.6.14 [6580 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 itcl3-dev amd64 3.4.4-2.1 [15.5 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libxss-dev amd64 1:1.2.3-1+b3 [22.7 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.47-1 [366 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.4-5 [47.8 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-2 [414 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libfontconfig1-dev amd64 2.15.0-2 [269 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b4 [35.8 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxft-dev amd64 2.3.6-1+b4 [73.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 tk8.6 amd64 8.6.16-1 [69.6 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 tk8.6-dev amd64 8.6.16-1 [794 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 tk amd64 8.6.14 [4076 B] Get: 88 http://deb.debian.org/debian unstable/main amd64 tk-dev amd64 8.6.14 [3896 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 itk3-dev amd64 3.4.2-4 [5528 B] Get: 90 http://deb.debian.org/debian unstable/main amd64 iwidgets4 all 4.1.1-2.1 [195 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 94 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-1 [105 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-1 [353 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 tklib all 0.9-1 [1749 kB] Fetched 56.6 MB in 3s (18.8 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19783 files and directories currently installed.) Preparing to unpack .../000-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../001-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../002-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../003-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 .../004-libpng16-16t64_1.6.47-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.47-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../006-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 .../007-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../008-fontconfig-config_2.15.0-2_amd64.deb ... Unpacking fontconfig-config (2.15.0-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../009-libfontconfig1_2.15.0-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../010-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 .../011-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 .../012-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 .../013-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../014-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../015-libxrender1_1%3a0.9.10-1.1+b4_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b4) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../016-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 .../017-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 .../018-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../019-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../020-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package itcl3:amd64. Preparing to unpack .../021-itcl3_3.4.4-2.1_amd64.deb ... Unpacking itcl3:amd64 (3.4.4-2.1) ... Selecting previously unselected package itk3:amd64. Preparing to unpack .../022-itk3_3.4.2-4_amd64.deb ... Unpacking itk3:amd64 (3.4.2-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../023-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../024-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../025-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../026-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../027-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../028-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../029-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../030-bsdextrautils_2.40.4-5_amd64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../031-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../032-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../033-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../034-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../035-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../036-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../037-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../038-libcom-err2_1.47.2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../039-comerr-dev_2.1-1.47.2-1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../040-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../041-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../042-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../043-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../044-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../045-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../046-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../047-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../048-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../049-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../050-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-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 .../053-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../055-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 .../056-tcl8.6_8.6.16+dfsg-1_amd64.deb ... 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Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+24) ... 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) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 7 18:08:54 UTC 2026. Universal Time is now: Tue Apr 7 18:08:54 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libhtscodecs-dev:amd64 (1.6.1-2) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up uuid-dev:amd64 (2.40.4-5) ... Setting up libncurses6:amd64 (6.5+20250216-1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.4.1-1) ... Setting up libpng16-16t64:amd64 (1.6.47-1) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.6.4-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... 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 (1.14.1-2) ... Setting up tcl8.6 (8.6.16+dfsg-1) ... Setting up libncurses-dev:amd64 (6.5+20250216-1) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up tcl8.6-dev:amd64 (8.6.16+dfsg-1) ... Setting up libpng-dev:amd64 (1.6.47-1) ... Setting up itcl3:amd64 (3.4.4-2.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... 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 (2.6.9+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up tcl (8.6.14) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up itcl3-dev:amd64 (3.4.4-2.1) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up man-db (2.13.0-1) ... 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 (3.8.9-2) ... Setting up itk3:amd64 (3.4.2-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up iwidgets4 (4.1.1-2.1) ... Setting up tcl-dev:amd64 (8.6.14) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up tk8.6 (8.6.16-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up libfontconfig-dev:amd64 (2.15.0-2) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-3) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libxss-dev:amd64 (1:1.2.3-1+b3) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up tk (8.6.14) ... Setting up libxft-dev:amd64 (2.3.6-1+b4) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libfontconfig1-dev:amd64 (2.15.0-2) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up tklib (0.9-1) ... Setting up tk8.6-dev:amd64 (8.6.16-1) ... Setting up itk3-dev:amd64 (3.4.2-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.12.1-3) ... Setting up tk-dev:amd64 (8.6.14) ... Setting up libstaden-read-dev (1.15.0-1.1+b2) ... Processing triggers for libc-bin (2.41-3) ... 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 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+b11-5_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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... 8.12.1 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 gcc option to enable large file support... 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-6.12.12+bpo-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 -j12 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./Misc SUBDIR=Misc all cd trev && make -f /build/reproducible-path/staden-2.0.0+b11/./trev/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./trev SUBDIR=trev all cd primer3 && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/trev' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/primer3' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[2]: warning: -j12 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/./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 -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' 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 -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 -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 /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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 Nothing to build for spin_emboss. 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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 Nothing to build for data. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' Nothing to build for scripts. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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 -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 -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 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 -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 -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 -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 -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 -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 -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 primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 '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 ()); | ~~~~~~~~~~~~~~~~~ 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 ()); | ~~~~~~~~~~~~~~~~~ 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 ()); | ~~~~~~~~~~~~~~~~~ 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 -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 -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 tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi all cd alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./alf SUBDIR=alf all cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g all cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/tk_utils' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/text_utils' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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: -j12 forced in submake: resetting jobserver mode. cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/g' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j12 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 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 ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' 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)) | ^~~ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' 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 alfsplit alfsplit.o -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 -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 -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 -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 -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 -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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' 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/eba' 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 ()); | ~~~~~~~~~~~~~~~~~ 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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 -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 -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 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 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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' 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/abi' 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 -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 -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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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: -j12 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 sequence_formats.c: In function 'get_embl_format_seq': sequence_formats.c:729:29: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 729 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:33: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 738 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function 'add_feat': sequence_formats.c:481:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 481 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 510 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 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 -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 -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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin all cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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: -j12 forced in submake: resetting jobserver mode. cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops all cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/vector_clip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/spin' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[2]: warning: -j12 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 -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 -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 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 -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 -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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 -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 -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 -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 -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 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 -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 -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 -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 -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 -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 -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 -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 -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 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 -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 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 -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 -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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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; | ^ seq_raster.c: In function 'seq_raster_callback': 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; | ^ 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 -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 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 -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 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 -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 -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 seq_reg_cmds.c: In function 'GetActiveSeqName': seq_reg_cmds.c:919:32: warning: zero-length gnu_printf format string [-Wformat-zero-length] 919 | vTcl_SetResult(interp, ""); | ^~ gcc -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 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; | ^ 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 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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 -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 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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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/stops' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' 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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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 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; | ^ 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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' 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 ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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_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; | ^ emboss_input_funcs.c: In function 'read_emboss_data_file': emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 402 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 444 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 477 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function 'init_emboss_stick_create': emboss_input_funcs.c:658:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 658 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 659 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ 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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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; | ^ 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; | ^ sip_quick_scan.c: In function 'quick_scan_callback': 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 -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 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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; | ^ 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 -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 -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 -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 -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 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; | ^ 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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; | ^ 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 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 -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 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 -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 -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 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 -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 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; | ^ 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 -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 -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 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 -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 -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 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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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 -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 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) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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/tracediff' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[2]: warning: -j12 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 -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 cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all 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 -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap4' make[2]: warning: -j12 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 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)) | ^~~~~ /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 -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 -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 -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 -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 -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 -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 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 -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 -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 -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 /usr/bin/ld: warning: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 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 -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 -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 -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 -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 -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 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 -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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 -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 -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 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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 ()); | ~~~~~~~~~~~~~~~~~ /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/./gap5/tg_index_common.c:105:(.text+0x592): warning: the use of `tmpnam' is dangerous, better use `mkstemp' 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 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); | ^ 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; | ^ 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); | ^ 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 -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 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; | ^ 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); | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 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 -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 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; | ^ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' 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); | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from vseqs.c:3: vseqs.c: In function 'new_vcontig': 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)) | ^~~ 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 ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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 ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -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 copy_db_main.c: In function 'main': copy_db_main.c:86:9: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 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 -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 -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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2435053 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: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[2]: warning: -j12 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 main.c: In function 'get_db': main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 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 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) /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 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 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 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 -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 -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 /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) 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 -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 -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 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 -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 -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[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' 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 -j12 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts install cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: warning: -j12 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' 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 install trev /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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' /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' install pregap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 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' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/Misc' mkdir /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/spin_emboss mkdir /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/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 cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/./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 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 cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/./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 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/./trev/trevrc /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/tk_utils' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/abi' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba 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/g' make[4]: warning: -j12 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates 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/eba' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' cp alfsplit /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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 cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins install cp: cp getABISampleName getABIcomment getABIdate getABIfield /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cannot stat '/build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' 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 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' 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 cp init_exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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/spin_emboss' 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 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/init_exp' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' 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/g' cp get_scf_field /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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 hetins /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/gcodes make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' 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: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' 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/./pregap4/pregap4rc /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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/stash /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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 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 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' 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 cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/m13mp18_primers /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: -j12 forced in submake: resetting jobserver mode. 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' 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/./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/seq_utils' cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./qclip SUBDIR=qclip install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops install cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/qclip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/find_renz' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' 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 install spin /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 cp make_weights /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 cp stops /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/tcl/spin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' cp find_renz /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' 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/mutlib' 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/find_renz' cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap4' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[4]: warning: -j12 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 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 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 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo2438721 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/prefinish' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[4]: warning: -j12 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/copy_reads mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp staden_convert /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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 install copy_reads /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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' 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/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/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 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/./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/haplo' 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-dbgsym' in '../staden-dbgsym_2.0.0+b11-5_amd64.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-5_all.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-5_amd64.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-5_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/2429740 and its subdirectories I: Current time: Tue Apr 7 06:09:53 -12 2026 I: pbuilder-time-stamp: 1775585393 Wed Mar 5 11:46:56 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Wed Mar 5 11:46:56 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Wed Mar 5 11:48:34 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Wed Mar 5 11:48:35 UTC 2025 I: staden_2.0.0+b11-5_amd64.changes: Format: 1.8 Date: Wed, 13 Mar 2024 15:32:32 +0100 Source: staden Binary: staden staden-common staden-dbgsym Architecture: all amd64 Version: 2.0.0+b11-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: staden - DNA sequence assembly (Gap4/Gap5), editing and analysis tools staden-common - Architecture independent files for Staden Closes: 1066508 Changes: staden (2.0.0+b11-5) unstable; urgency=medium . * Team upload. * Mark staden-commen as Multi-Arch: foreign * Standards-Version: 4.5.0 * Correctly detect 64bit host architectures * d/patches/use_mkstemp_instead_of_tmpnam.patch: add missing stdlib include. Closes: #1066508 * d/control: libncurses-dev replaced libncurses5-dev. * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * Rules-Requires-Root: no (routine-update) * No tab in license text (routine-update) * Update lintian override info format in d/staden-common.lintian-overrides on line 2. * watch file standard 4 (routine-update) * d/upstream/metadata: add links to Sourceforge issue tracker, VCS Checksums-Sha1: be38c1dad5e6214e5387532b4df1269ac134c37f 1970864 staden-common_2.0.0+b11-5_all.deb bcf5603ad83e72aee53953db1ccb810a76365a49 4453768 staden-dbgsym_2.0.0+b11-5_amd64.deb abdd5ccae49571e3c09d85d34a9fb87934d2f40c 8721 staden_2.0.0+b11-5_amd64.buildinfo 90f06ed3a7f74d3e114c7ba3f9299d223de89665 1656720 staden_2.0.0+b11-5_amd64.deb Checksums-Sha256: ecff8239a1d8689692cff37d3acbdadb18117fe9ce3676ae9a4128abd4690f37 1970864 staden-common_2.0.0+b11-5_all.deb 0ae4fb2d7c4f1757f3ffc59abf45272e4bb8deafb703dbf1fd93a164de197c45 4453768 staden-dbgsym_2.0.0+b11-5_amd64.deb 89a75700ee6d3cf91bc18fe1890d5b44c8fbb47c64c38de63eefb8b8e6b78733 8721 staden_2.0.0+b11-5_amd64.buildinfo f45a83e4a3658615b3f79e4a66f2256b10b17b52ff6dca2c82c337d68a0a6345 1656720 staden_2.0.0+b11-5_amd64.deb Files: defa0dcba7c528911beac1c3820609a2 1970864 science optional staden-common_2.0.0+b11-5_all.deb ae53986deff52562498b10f84dadbe46 4453768 debug optional staden-dbgsym_2.0.0+b11-5_amd64.deb 03494d31f53c9cf14085e89feda25ab2 8721 science optional staden_2.0.0+b11-5_amd64.buildinfo 229ee0d7f4f0f0ee8a706d361f876e63 1656720 science optional staden_2.0.0+b11-5_amd64.deb Wed Mar 5 11:48:36 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_38-49398.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/staden_2.0.0+b11-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/staden_2.0.0+b11-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/staden_2.0.0+b11-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/b1/staden_2.0.0+b11-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wlj8N73S/b2/staden_2.0.0+b11-5_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 Service runtime: 226ms CPU time consumed: 226ms Wed Mar 5 11:48:37 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Wed Mar 5 11:48:37 UTC 2025 I: staden from unstable built successfully and reproducibly on amd64. Wed Mar 5 11:48:39 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Mar 5 11:48:39 UTC 2025 I: Submitting 12K b1/staden_2.0.0+b11-5_amd64.buildinfo.asc Wed Mar 5 11:48:39 UTC 2025 I: Submitting 12K b2/staden_2.0.0+b11-5_amd64.buildinfo.asc Wed Mar 5 11:48:40 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Mar 5 11:48:40 UTC 2025 I: Done submitting .buildinfo files. Wed Mar 5 11:48:40 UTC 2025 I: Removing signed staden_2.0.0+b11-5_amd64.buildinfo.asc files: removed './b1/staden_2.0.0+b11-5_amd64.buildinfo.asc' removed './b2/staden_2.0.0+b11-5_amd64.buildinfo.asc'