Fri May 24 21:17:53 UTC 2024 I: starting to build staden/trixie/arm64 on jenkins on '2024-05-24 21:17' Fri May 24 21:17:53 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_21/13071/console.log Fri May 24 21:17:53 UTC 2024 I: Downloading source for trixie/staden=2.0.0+b11-5 --2024-05-24 21:17:53-- 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% 317M=0s 2024-05-24 21:17:53 (317 MB/s) - ‘staden_2.0.0+b11-5.dsc’ saved [2185/2185] Fri May 24 21:17:53 UTC 2024 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----- Fri May 24 21:17:53 UTC 2024 I: Checking whether the package is not for us Fri May 24 21:17:53 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Fri May 24 21:17:53 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Fri May 24 21:19:32 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 26 15:40:56 -12 2025 I: pbuilder-time-stamp: 1750995656 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 gpgv: Signature made Wed Mar 13 14:41:11 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./staden_2.0.0+b11-5.dsc: no acceptable signature found dpkg-source: info: extracting staden in staden-2.0.0+b11 dpkg-source: info: unpacking staden_2.0.0+b11.orig.tar.gz dpkg-source: info: unpacking staden_2.0.0+b11-5.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/2138125/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7c1ee2c0648647b8b4915f376e1f000a' 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='2138125' 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.EI6aHT6t/pbuilderrc_2bqU --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 24 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2138125/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: arm64 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 ... 19746 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} 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} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdata-optlist-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libgssapi-krb5-2{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstaden-read-dev{a} libstaden-read14t64{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libtcl8.6{a} libtk8.6{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft-dev{a} libxft2{a} libxml2{a} libxrender-dev{a} libxrender1{a} libxss-dev{a} libxss1{a} m4{a} man-db{a} 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 lynx publicsuffix tcllib wget 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 41.3 MB of archives. After unpacking 149 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 itcl3 arm64 3.4.4-2+b1 [46.9 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 itk3 arm64 3.4.2-3.1+b1 [26.5 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libsub-prototype-perl arm64 0.03-2+b2 [9776 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 52 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 tcl8.6 arm64 8.6.14+dfsg-1 [120 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 tcl8.6-dev arm64 8.6.14+dfsg-1 [1001 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 tcl arm64 8.6.14 [4032 B] Get: 64 http://deb.debian.org/debian trixie/main arm64 tcl-dev arm64 8.6.14 [6572 B] Get: 65 http://deb.debian.org/debian trixie/main arm64 itcl3-dev arm64 3.4.4-2+b1 [15.6 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 libxau-dev arm64 1:1.0.9-1+b1 [21.5 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libxdmcp-dev arm64 1:1.1.2-3+b1 [40.6 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libxcb1-dev arm64 1.17.0-2 [183 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libx11-dev arm64 2:1.8.7-1+b1 [861 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libxext-dev arm64 2:1.3.4-1+b1 [107 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libxss-dev arm64 1:1.2.3-1+b1 [22.8 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b3 [308 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libpng-dev arm64 1.6.43-5 [356 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libfreetype-dev arm64 2.13.2+dfsg-1+b4 [585 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 uuid-dev arm64 2.40.1-1 [44.5 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libfontconfig-dev arm64 2.15.0-1.1 [410 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libfontconfig1-dev arm64 2.15.0-1.1 [269 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b1 [35.5 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libxft-dev arm64 2.3.6-1+b1 [71.5 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 tk8.6 arm64 8.6.14-1 [69.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 tk8.6-dev arm64 8.6.14-1 [755 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 tk arm64 8.6.14 [4076 B] Get: 92 http://deb.debian.org/debian trixie/main arm64 tk-dev arm64 8.6.14 [3892 B] Get: 93 http://deb.debian.org/debian trixie/main arm64 itk3-dev arm64 3.4.2-3.1+b1 [5540 B] Get: 94 http://deb.debian.org/debian trixie/main arm64 iwidgets4 all 4.1.1-2.1 [195 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 99 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-5 [524 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libhtscodecs-dev arm64 1.6.0-1+b1 [2976 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5-2 [337 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libstaden-read14t64 arm64 1.15.0-1.1+b1 [249 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libstaden-read-dev arm64 1.15.0-1.1+b1 [332 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 tklib all 0.8~20240305-1 [1591 kB] Fetched 41.3 MB in 0s (147 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19746 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../001-libtcl8.6_8.6.14+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../002-libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../003-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../004-libpng16-16t64_1.6.43-5_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../005-libfreetype6_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... 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_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../009-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../010-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../011-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../012-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../013-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../014-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../015-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../017-libxft2_2.3.6-1+b1_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../018-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../019-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../020-libxss1_1%3a1.2.3-1+b1_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../021-libtk8.6_8.6.14-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.14-1) ... Selecting previously unselected package itcl3:arm64. Preparing to unpack .../022-itcl3_3.4.4-2+b1_arm64.deb ... Unpacking itcl3:arm64 (3.4.4-2+b1) ... Selecting previously unselected package itk3:arm64. Preparing to unpack .../023-itk3_3.4.2-3.1+b1_arm64.deb ... Unpacking itk3:arm64 (3.4.2-3.1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../024-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../025-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../026-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../027-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../028-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../029-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../030-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../031-bsdextrautils_2.40.1-1_arm64.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../032-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../033-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../034-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../035-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../036-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../037-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../038-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../039-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../040-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../041-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../042-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../043-libparams-util-perl_1.102-3_arm64.deb ... Unpacking libparams-util-perl (1.102-3) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../044-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../045-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../046-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libsub-prototype-perl. Preparing to unpack .../047-libsub-prototype-perl_0.03-2+b2_arm64.deb ... Unpacking libsub-prototype-perl (0.03-2+b2) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../048-libsub-override-perl_0.11-1_all.deb ... Unpacking libsub-override-perl (0.11-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../049-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../050-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../051-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../052-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../053-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../054-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../055-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../056-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 .../057-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../058-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../059-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package tcl8.6. Preparing to unpack .../060-tcl8.6_8.6.14+dfsg-1_arm64.deb ... Unpacking tcl8.6 (8.6.14+dfsg-1) ... Selecting previously unselected package tcl8.6-dev:arm64. Preparing to unpack .../061-tcl8.6-dev_8.6.14+dfsg-1_arm64.deb ... Unpacking tcl8.6-dev:arm64 (8.6.14+dfsg-1) ... Selecting previously unselected package tcl. Preparing to unpack .../062-tcl_8.6.14_arm64.deb ... Unpacking tcl (8.6.14) ... Selecting previously unselected package tcl-dev:arm64. Preparing to unpack .../063-tcl-dev_8.6.14_arm64.deb ... Unpacking tcl-dev:arm64 (8.6.14) ... Selecting previously unselected package itcl3-dev:arm64. Preparing to unpack .../064-itcl3-dev_3.4.4-2+b1_arm64.deb ... Unpacking itcl3-dev:arm64 (3.4.4-2+b1) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../065-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../066-x11proto-dev_2024.1-1_all.deb ... Unpacking x11proto-dev (2024.1-1) ... Selecting previously unselected package x11proto-core-dev. Preparing to unpack .../067-x11proto-core-dev_2024.1-1_all.deb ... Unpacking x11proto-core-dev (2024.1-1) ... Selecting previously unselected package libxau-dev:arm64. Preparing to unpack .../068-libxau-dev_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau-dev:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp-dev:arm64. Preparing to unpack .../069-libxdmcp-dev_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp-dev:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../070-xtrans-dev_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... Selecting previously unselected package libxcb1-dev:arm64. Preparing to unpack .../071-libxcb1-dev_1.17.0-2_arm64.deb ... Unpacking libxcb1-dev:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-dev:arm64. Preparing to unpack .../072-libx11-dev_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-dev:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext-dev:arm64. Preparing to unpack .../073-libxext-dev_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext-dev:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss-dev:arm64. Preparing to unpack .../074-libxss-dev_1%3a1.2.3-1+b1_arm64.deb ... Unpacking libxss-dev:arm64 (1:1.2.3-1+b1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../075-libexpat1-dev_2.6.2-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.2-1) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../076-libbrotli-dev_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../077-libbz2-dev_1.0.8-5.1_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-5.1) ... Selecting previously unselected package libpng-dev:arm64. Preparing to unpack .../078-libpng-dev_1.6.43-5_arm64.deb ... Unpacking libpng-dev:arm64 (1.6.43-5) ... Selecting previously unselected package libfreetype-dev:arm64. Preparing to unpack .../079-libfreetype-dev_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype-dev:arm64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package uuid-dev:arm64. Preparing to unpack .../080-uuid-dev_2.40.1-1_arm64.deb ... Unpacking uuid-dev:arm64 (2.40.1-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../081-libpkgconf3_1.8.1-1+b2_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../082-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../083-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Selecting previously unselected package libfontconfig-dev:arm64. Preparing to unpack .../084-libfontconfig-dev_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig-dev:arm64 (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1-dev:arm64. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 27 03:41:17 UTC 2025. Universal Time is now: Fri Jun 27 03:41:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libhtscodecs-dev:arm64 (1.6.0-1+b1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up uuid-dev:arm64 (2.40.1-1) ... Setting up libncurses6:arm64 (6.5-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up libtcl8.6:arm64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b3) ... Setting up libbz2-dev:arm64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up tcl8.6 (8.6.14+dfsg-1) ... Setting up libncurses-dev:arm64 (6.5-2) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libxau-dev:arm64 (1:1.0.9-1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up tcl8.6-dev:arm64 (8.6.14+dfsg-1) ... Setting up libpng-dev:arm64 (1.6.43-5) ... Setting up itcl3:arm64 (3.4.4-2+b1) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:arm64 (1:1.1.2-3+b1) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up groff-base (1.23.0-4) ... Setting up tcl (8.6.14) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up itcl3-dev:arm64 (3.4.4-2+b1) ... Setting up libxcb1-dev:arm64 (1.17.0-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libx11-dev:arm64 (2:1.8.7-1+b1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-5) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-5) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libfreetype-dev:arm64 (2.13.2+dfsg-1+b4) ... Setting up tcl-dev:arm64 (8.6.14) ... Setting up libxext-dev:arm64 (2:1.3.4-1+b1) ... Setting up libsub-override-perl (0.11-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b1) ... Setting up libxrender-dev:arm64 (1:0.9.10-1.1+b1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxft2:arm64 (2.3.6-1+b1) ... Setting up libfontconfig-dev:arm64 (2.15.0-1.1) ... Setting up libtk8.6:arm64 (8.6.14-1) ... Setting up libstaden-read14t64:arm64 (1.15.0-1.1+b1) ... Setting up libxss-dev:arm64 (1:1.2.3-1+b1) ... Setting up itk3:arm64 (3.4.2-3.1+b1) ... Setting up iwidgets4 (4.1.1-2.1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libxft-dev:arm64 (2.3.6-1+b1) ... Setting up tk8.6 (8.6.14-1) ... Setting up libfontconfig1-dev:arm64 (2.15.0-1.1) ... Setting up libstaden-read-dev (1.15.0-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up tk8.6-dev:arm64 (8.6.14-1) ... Setting up tk (8.6.14) ... Setting up itk3-dev:arm64 (3.4.2-3.1+b1) ... Setting up tk-dev:arm64 (8.6.14) ... Setting up tklib (0.8~20240305-1) ... Processing triggers for libc-bin (2.38-11) ... 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 arm64 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.m4:704: 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.m4:2847: 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.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:699: 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.m4:2847: 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.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:699: 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.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:699: AS_IF is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:2997: 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.m4:2847: 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.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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/aarch64-linux-gnu \ --with-itk=/usr/lib/tcltk/aarch64-linux-gnu ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-64bit --with-itcl=/usr/lib/tcltk/aarch64-linux-gnu --with-itk=/usr/lib/tcltk/aarch64-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... 8.7.1 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 special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no 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 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-6.1.0-21-cloud-arm64 checking for ar... ar checking if compiler accepts -m64 flag... no configure: WARNING: 64bit support being disabled -- don't know magic for this platform 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/tklib0.8) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/aarch64-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/aarch64-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/tklib0.8 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/aarch64-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/aarch64-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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -w -j12 --jobserver-auth=3,4 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 pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all 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/pregap4' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -w -j12 --jobserver-auth=3,4 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]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/./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' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/primer3' cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' 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 -mbranch-protection=standard -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 Nothing to build for Pregap4. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 /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' Nothing to build for data. Nothing to build for spin_emboss. 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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 /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' Nothing to build for scripts. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' 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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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:964, from primer3_main.c:7: In function 'sprintf', inlined from 'boulder_print_oligos' at primer3_main.c:416:7: /usr/include/aarch64-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:964, from parse_db.c:19: In function 'sprintf', inlined from 'parse_entry' at parse_db.c:234:7: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 33 and 8224 bytes into a destination of size 8192 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ primer3_main.c: In function 'main': primer3_main.c:234:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); | ^~ In function 'boulder_print_pairs', inlined from 'main' at primer3_main.c:109:3: primer3_main.c:234:30: note: directive argument in the range [1, 2147483646] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In function 'sprintf', inlined from 'boulder_print_pairs' at primer3_main.c:234:7, inlined from 'main' at primer3_main.c:109:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils 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 text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi 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 alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./alf SUBDIR=alf all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/abi' 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. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/g' 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 -mbranch-protection=standard -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 cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' 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 -w -j12 --jobserver-auth=3,4 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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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. cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins all 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkSheet_common.o -c tkSheet_common.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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:2567:60: note: in definition of macro 'Tcl_FindHashEntry' 2567 | (*((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:2570:62: note: in definition of macro 'Tcl_CreateHashEntry' 2570 | (*((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:2567:60: note: in definition of macro 'Tcl_FindHashEntry' 2567 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o postscript.o -c postscript.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -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/aarch64-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:964, from alfsplit.c:30: In function 'sprintf', inlined from 'main' at alfsplit.c:312:6: /usr/include/aarch64-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 -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceComp.o -c tkTraceComp.c gcc -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 -mbranch-protection=standard -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 -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/aarch64-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 -mbranch-protection=standard -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 -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -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 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/alf' gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/init_exp' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm 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:964, from tkTraceDisp.c:2: In function 'sprintf', inlined from 'trace_draw_numbers' at tkTraceDisp.c:746:6: /usr/include/aarch64-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/aarch64-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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' 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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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 -w -j12 --jobserver-auth=3,4 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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:964, from renz_utils.c:3: In function 'sprintf', inlined from 'SetREnzColour' at renz_utils.c:1049:5: /usr/include/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin all cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip 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 screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -w -j12 --jobserver-auth=3,4 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/vector_clip' 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. cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./qclip SUBDIR=qclip all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip 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 -mbranch-protection=standard -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 cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 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/polyA_clip' 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 -mbranch-protection=standard -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 cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' 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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -w -j12 --jobserver-auth=3,4 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/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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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; | ^ raster_cmds.c: In function 'RasterResults': seq_raster.c: In function 'seq_raster_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 -mbranch-protection=standard -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 raster_cmds.c:250:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 250 | zoom = (int)gen.result; | ^ 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; | ^ 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, ""); | ^~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 stops stops.o -ltext_utils -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' 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 -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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; | ^ 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 -mbranch-protection=standard -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 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); | ^~~~~~~~~~~~~~~~~~~~~~ sp_alignment.cpp: In function 'void sp::store_hashn(Hash*)': sp_alignment.cpp:754:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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:964, 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/aarch64-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/aarch64-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 -mbranch-protection=standard -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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; | ^ sip_find_identity.c: In function 'identities_callback': sip_find_identity.c:210:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 210 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 sip_quick_scan.c: In function 'quick_scan_callback': sip_quick_scan.c:234:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 234 | jdata->info.result = (void *)id; | ^ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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_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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 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; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 nip_stop_codon.c: In function 'nip_stop_codons_callback': nip_stop_codon.c:195:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 195 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 nip_wtmatrix_search.c: In function 'nip_wtmatrix_search_callback': nip_wtmatrix_search.c:167:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 167 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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:964, 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/aarch64-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 ()); | ~~~~~~~~~~~~~~~~~ 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 function 'sprintf', inlined from 'StringMatch' at find_oligo.c:957:4: /usr/include/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 cp /build/reproducible-path/staden-2.0.0+b11/./mutlib/mutlib.def 2>&- gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[2]: [/build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile:81: /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutscan SUBDIR=mutscan all cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 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/gap4' 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 -mbranch-protection=standard -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tracediff -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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:2553:69: note: in definition of macro 'Tcl_SetHashValue' 2553 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (ClientData) (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:2553:69: note: in definition of macro 'Tcl_SetHashValue' 2553 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (ClientData) (value)) | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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) { | ^ /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 -mbranch-protection=standard -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 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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 /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 -mbranch-protection=standard -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 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:964, 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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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:964, from readpair.c:18: In function 'sprintf', inlined from 'readpair_obj_func' at readpair.c:175:3: /usr/include/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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:964, 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/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/./gap5/tg_index_common.c:105:(.text+0x5b8): warning: the use of `tmpnam' is dangerous, better use `mkstemp' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm 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:964, from copy_db.c:1: In function 'sprintf', inlined from 'copy_read_name' at copy_db.c:118:3: /usr/include/aarch64-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 ()); | ~~~~~~~~~~~~~~~~~ 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; | ^ /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) 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:964, 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/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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); | ^ 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 -mbranch-protection=standard -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 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); | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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:964, 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/aarch64-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 ()); | ~~~~~~~~~~~~~~~~~ strand_coverage.c: In function 'strand_coverage_callback': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 strand_coverage.c:503:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 503 | jdata->generic.data = (void *)scov->cons_id; | ^ strand_coverage.c:541:49: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 541 | strand_coverage_join(io, c, scov, (int)jdata->generic.data); | ^ 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:2570:62: note: in definition of macro 'Tcl_CreateHashEntry' 2570 | (*((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:2570:62: note: in definition of macro 'Tcl_CreateHashEntry' 2570 | (*((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:2567:60: note: in definition of macro 'Tcl_FindHashEntry' 2567 | (*((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:2567:60: note: in definition of macro 'Tcl_FindHashEntry' 2567 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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:964, 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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/aarch64-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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd copy_reads && make -f /build/reproducible-path/staden-2.0.0+b11/./copy_reads/Makefile -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 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/copy_reads' make[2]: warning: -j12 forced in submake: resetting jobserver mode. 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/convert' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd haplo && make -f /build/reproducible-path/staden-2.0.0+b11/./haplo/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./haplo SUBDIR=haplo all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 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:964, from copy_reads.c:4: In function 'sprintf', inlined from 'create_si_struct' at copy_reads.c:125:5: /usr/include/aarch64-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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 '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/aarch64-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/aarch64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ldgcc -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/aarch64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm : 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/aarch64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/aarch64-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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-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/copy_reads' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/haplo' 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-linux-gnu -ltk8.6 -L/usr/lib/aarch64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' 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/aarch64-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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -w -j12 --jobserver-auth=3,4 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/primer3' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[4]: warning: -j12 forced in submake: resetting jobserver mode. install trev /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libmisc.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install 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 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/Misc' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3' 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -w -j12 --jobserver-auth=3,4 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/spin_emboss' cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts install 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/libprimer3.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' install pregap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data 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 /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules /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' /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' 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes 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/./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/tcl/spin_emboss/acdtcl 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/./data/alus/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cp /build/reproducible-path/staden-2.0.0+b11/./scripts/fasta2exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts 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 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 /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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' cp: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cp: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory 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 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/./data/blast_data/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data 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 cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -w -j12 --jobserver-auth=3,4 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/spin_emboss' cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' 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. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes 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 cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./alf SUBDIR=alf 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. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors cp /build/reproducible-path/staden-2.0.0+b11/lib/libtext_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden 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/lib/libtk_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g install 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/text_utils' 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/./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 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 cp getABISampleName getABIcomment getABIdate getABIfield /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp alfsplit /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba install make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/stash /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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/renzyme_bairoch /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./data/m13mp18_primers /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install cp /build/reproducible-path/staden-2.0.0+b11/lib/libg.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -w -j12 --jobserver-auth=3,4 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' 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/./data/vector_primer /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/get_scf_field' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp eba /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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/eba' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -w -j12 --jobserver-auth=3,4 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 init_exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' cp get_scf_field /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp hetins /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' 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/aarch64-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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' make[4]: warning: -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. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install cp /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden cp vector_clip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -w -j12 --jobserver-auth=3,4 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/screen_seq' make[4]: warning: -j12 forced in submake: resetting jobserver mode. install spin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin 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 stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install cp qclip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install cp screen_seq /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' 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]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -w -j12 --jobserver-auth=3,4 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/mutscan' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install cp /build/reproducible-path/staden-2.0.0+b11/./spin/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp polyA_clip /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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' cp stops /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install cp find_renz /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 cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install 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/find_renz' 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/polyA_clip' 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/gap4' 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/aarch64-linux-gnu/staden cp tracediff /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin install gap5 /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' 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 /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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' 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 cp /build/reproducible-path/staden-2.0.0+b11/lib/libgap5.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden cp tg_index.bin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin install tg_index /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp copy_db /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 install gap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' 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 /build/reproducible-path/staden-2.0.0+b11/lib/libgap.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden 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 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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 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 -w -j12 --jobserver-auth=3,4 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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/copy_reads' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -w -j12 --jobserver-auth=3,4 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/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/prefinish mkdir /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/./prefinish/*.tcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itk /build/reproducible-path/staden-2.0.0+b11/./prefinish/help /build/reproducible-path/staden-2.0.0+b11/./prefinish/args.template /build/reproducible-path/staden-2.0.0+b11/./prefinish/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish install copy_reads /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp staden_convert /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' 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/aarch64-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/./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/aarch64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' install prefinish /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo 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/./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 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/lib/libhaplo.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/aarch64-linux-gnu/staden 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 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 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/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/aarch64-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/aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-5_all.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-5_arm64.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-5_arm64.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-5_arm64.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/2138125 and its subdirectories I: Current time: Thu Jun 26 15:42:31 -12 2025 I: pbuilder-time-stamp: 1750995751 Fri May 24 21:19:33 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Fri May 24 21:19:33 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Fri May 24 21:21:15 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Fri May 24 21:21:16 UTC 2024 I: staden_2.0.0+b11-5_arm64.changes: Format: 1.8 Date: Wed, 13 Mar 2024 15:32:32 +0100 Source: staden Binary: staden staden-common staden-dbgsym Architecture: all arm64 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: ba80749e4e2ffca66e02f743d90fa054c6590ffc 1970956 staden-common_2.0.0+b11-5_all.deb 6ae317cea441650a50d758df10c4916f0ab9b4fc 4383836 staden-dbgsym_2.0.0+b11-5_arm64.deb 5a857eb7f3318a1eab00a87e0519ed0fd291ebb2 8203 staden_2.0.0+b11-5_arm64.buildinfo bd21dd634311311685987b574ffc49ccee93f671 1515144 staden_2.0.0+b11-5_arm64.deb Checksums-Sha256: cb245f65637de8b5828f28e5d0f86ee745a4f41882b1ccc1ab917aabcb16ee50 1970956 staden-common_2.0.0+b11-5_all.deb eb8698fd7f890c5ffdd60839d5101c1afeb140565637970c0cc3e21d265d76b3 4383836 staden-dbgsym_2.0.0+b11-5_arm64.deb 0b0c7d28d164bfc9ee1f71c84087edcaf6ee552bc517475c68d686bdd7111972 8203 staden_2.0.0+b11-5_arm64.buildinfo 1d738670468268182ae8753ff3282f3dd9da60fa3de5c369506adebdfce730ba 1515144 staden_2.0.0+b11-5_arm64.deb Files: a561b490dfaebecef63cde2fe80e4c87 1970956 science optional staden-common_2.0.0+b11-5_all.deb 5469e9c7d6779a549f401c3e26833b51 4383836 debug optional staden-dbgsym_2.0.0+b11-5_arm64.deb c9da14cb831a3aee56666ea0529fc5ee 8203 science optional staden_2.0.0+b11-5_arm64.buildinfo 1007a28ed8d3f9133e0c5e32842e4008 1515144 science optional staden_2.0.0+b11-5_arm64.deb Fri May 24 21:21:17 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_21-13071.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/staden_2.0.0+b11-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/staden_2.0.0+b11-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/staden_2.0.0+b11-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/b1/staden_2.0.0+b11-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EI6aHT6t/b2/staden_2.0.0+b11-5_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.448s) 0.448s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.101s) 0.101s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 791ms CPU time consumed: 792ms Fri May 24 21:21:18 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Fri May 24 21:21:18 UTC 2024 I: staden from trixie built successfully and reproducibly on arm64. Fri May 24 21:21:19 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 24 21:21:19 UTC 2024 I: Submitting 12K b1/staden_2.0.0+b11-5_arm64.buildinfo.asc Fri May 24 21:21:20 UTC 2024 I: Submitting 12K b2/staden_2.0.0+b11-5_arm64.buildinfo.asc Fri May 24 21:21:21 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 24 21:21:21 UTC 2024 I: Done submitting .buildinfo files. Fri May 24 21:21:21 UTC 2024 I: Removing signed staden_2.0.0+b11-5_arm64.buildinfo.asc files: removed './b1/staden_2.0.0+b11-5_arm64.buildinfo.asc' removed './b2/staden_2.0.0+b11-5_arm64.buildinfo.asc'