I: pbuilder: network access will be disabled during build I: Current time: Wed Mar 11 07:33:02 -12 2026 I: pbuilder-time-stamp: 1773257582 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [staden_2.0.0+b11-5.dsc] I: copying [./staden_2.0.0+b11.orig.tar.gz] I: copying [./staden_2.0.0+b11-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden_2.0.0+b11-5.dsc: unsupported subcommand dpkg-source: info: extracting staden in staden-2.0.0+b11 dpkg-source: info: unpacking staden_2.0.0+b11.orig.tar.gz dpkg-source: info: unpacking staden_2.0.0+b11-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying make_help_menus_work.patch dpkg-source: info: applying fix_tcl_path.patch dpkg-source: info: applying fix_awk.patch dpkg-source: info: applying enable_setting_stadenroot.patch dpkg-source: info: applying include_xalloc.patch dpkg-source: info: applying use_mkstemp_instead_of_tmpnam.patch dpkg-source: info: applying fix_implicit_declaration.patch dpkg-source: info: applying autoconfig.patch dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3146679/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='583fa9bf96924070a8410aa9abad3909' 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='3146679' 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.LYsHTmt3/pbuilderrc_DSyo --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LYsHTmt3/b1 --logfile b1/build.log staden_2.0.0+b11-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3146679/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libstaden-read-dev, itcl3-dev, itk3-dev, zlib1g-dev, libbz2-dev, liblzma-dev, tcl-dev, tk-dev, tklib, libpng-dev, libncurses-dev, iwidgets4, libcurl4-gnutls-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19806 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev; however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on itcl3-dev; however: Package itcl3-dev is not installed. pbuilder-satisfydepends-dummy depends on itk3-dev; however: Package itk3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on tcl-dev; however: Package tcl-dev is not installed. pbuilder-satisfydepends-dummy depends on tk-dev; however: Package tk-dev is not installed. pbuilder-satisfydepends-dummy depends on tklib; however: Package tklib is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on iwidgets4; however: Package iwidgets4 is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} itcl3{a} itcl3-dev{a} itk3{a} itk3-dev{a} iwidgets4{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstaden-read-dev{a} libstaden-read14t64{a} libtasn1-6{a} libtasn1-6-dev{a} libtcl8.6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft-dev{a} libxft2{a} libxml2{a} libxrender-dev{a} libxrender1{a} libxss-dev{a} libxss1{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tcl{a} tcl-dev{a} tcl8.6{a} tcl8.6-dev{a} tk{a} tk-dev{a} tk8.6{a} tk8.6-dev{a} tklib{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules libtasn1-doc lynx publicsuffix tcllib wget 0 packages upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 56.5 MB of archives. After unpacking 195 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 itcl3 amd64 3.4.4-2.1 [48.1 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 itk3 amd64 3.4.2-4 [26.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 tcl8.6 amd64 8.6.16+dfsg-1 [121 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 tcl8.6-dev amd64 8.6.16+dfsg-1 [1032 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 tcl amd64 8.6.14 [4032 B] Get: 60 http://deb.debian.org/debian unstable/main amd64 tcl-dev amd64 8.6.14 [6580 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 itcl3-dev amd64 3.4.4-2.1 [15.5 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libxss-dev amd64 1:1.2.3-1+b3 [22.7 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.46-4 [370 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.4-3 [47.6 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-2 [414 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libfontconfig1-dev amd64 2.15.0-2 [269 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b4 [35.8 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxft-dev amd64 2.3.6-1+b4 [73.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 tk8.6 amd64 8.6.16-1 [69.6 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 tk8.6-dev amd64 8.6.16-1 [794 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 tk amd64 8.6.14 [4076 B] Get: 88 http://deb.debian.org/debian unstable/main amd64 tk-dev amd64 8.6.14 [3896 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 itk3-dev amd64 3.4.2-4 [5528 B] Get: 90 http://deb.debian.org/debian unstable/main amd64 iwidgets4 all 4.1.1-2.1 [195 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 94 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1+b1 [475 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-1 [3000 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 tklib all 0.9-1 [1749 kB] Fetched 56.5 MB in 2s (32.6 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19806 files and directories currently installed.) Preparing to unpack .../000-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../001-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... Selecting previously unselected package libexpat1:amd64. 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Unpacking tcl8.6 (8.6.16+dfsg-1) ... Selecting previously unselected package tcl8.6-dev:amd64. Preparing to unpack .../057-tcl8.6-dev_8.6.16+dfsg-1_amd64.deb ... Unpacking tcl8.6-dev:amd64 (8.6.16+dfsg-1) ... Selecting previously unselected package tcl. Preparing to unpack .../058-tcl_8.6.14_amd64.deb ... Unpacking tcl (8.6.14) ... Selecting previously unselected package tcl-dev:amd64. Preparing to unpack .../059-tcl-dev_8.6.14_amd64.deb ... Unpacking tcl-dev:amd64 (8.6.14) ... Selecting previously unselected package itcl3-dev:amd64. Preparing to unpack .../060-itcl3-dev_3.4.4-2.1_amd64.deb ... Unpacking itcl3-dev:amd64 (3.4.4-2.1) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../061-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../062-x11proto-dev_2024.1-1_all.deb ... Unpacking x11proto-dev (2024.1-1) ... 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Selecting previously unselected package libxext-dev:amd64. Preparing to unpack .../069-libxext-dev_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext-dev:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxss-dev:amd64. Preparing to unpack .../070-libxss-dev_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss-dev:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../071-libexpat1-dev_2.6.4-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../072-libbrotli-dev_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../073-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libpng-dev:amd64. Preparing to unpack .../074-libpng-dev_1.6.46-4_amd64.deb ... Unpacking libpng-dev:amd64 (1.6.46-4) ... Selecting previously unselected package libfreetype-dev:amd64. Preparing to unpack .../075-libfreetype-dev_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package uuid-dev:amd64. Preparing to unpack .../076-uuid-dev_2.40.4-3_amd64.deb ... Unpacking uuid-dev:amd64 (2.40.4-3) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../077-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../078-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../079-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package libfontconfig-dev:amd64. Preparing to unpack .../080-libfontconfig-dev_2.15.0-2_amd64.deb ... 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Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Mar 11 19:34:25 UTC 2026. Universal Time is now: Wed Mar 11 19:34:25 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libhtscodecs-dev:amd64 (1.6.1-1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up uuid-dev:amd64 (2.40.4-3) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.4.0-2) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libnghttp3-dev:amd64 (1.6.0-2) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up tcl8.6 (8.6.16+dfsg-1) ... Setting up libncurses-dev:amd64 (6.5+20250125-2) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up tcl8.6-dev:amd64 (8.6.16+dfsg-1) ... Setting up libpng-dev:amd64 (1.6.46-4) ... Setting up itcl3:amd64 (3.4.4-2.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libldap-dev:amd64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up tcl (8.6.14) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up itcl3-dev:amd64 (3.4.4-2.1) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up itk3:amd64 (3.4.2-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up iwidgets4 (4.1.1-2.1) ... Setting up tcl-dev:amd64 (8.6.14) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up tk8.6 (8.6.16-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up libfontconfig-dev:amd64 (2.15.0-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libxss-dev:amd64 (1:1.2.3-1+b3) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up tk (8.6.14) ... Setting up libxft-dev:amd64 (2.3.6-1+b4) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libfontconfig1-dev:amd64 (2.15.0-2) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up tklib (0.9-1) ... Setting up tk8.6-dev:amd64 (8.6.16-1) ... Setting up itk3-dev:amd64 (3.4.2-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.1-1+b1) ... Setting up tk-dev:amd64 (8.6.14) ... Setting up libstaden-read-dev (1.15.0-1.1+b2) ... Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/staden-2.0.0+b11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden_2.0.0+b11-5_source.changes dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' make spotless || true make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' make[2]: *** No rule to make target 'spotless'. Stop. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' rm -f config.log config.status rm -f Makefile shlib.conf staden_config.h system.mk find -name debian -prune -o -name .dir -exec rm '{}' ';' make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:32: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:32: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/libcurl_check_config.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.in:32: the top level configure.in:33: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:33: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_zlib.m4:32: AX_LIB_ZLIB is expanded from... configure.in:33: the top level configure.in:34: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:34: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_lzma.m4:32: AX_LIB_LZMA is expanded from... configure.in:34: the top level configure.in:35: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:35: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_png.m4:34: AX_LIB_PNG is expanded from... configure.in:35: the top level configure.in:40: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:40: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_staden_io_lib.m4:35: AX_LIB_IO_LIB is expanded from... configure.in:40: the top level configure.in:43: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:43: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_curses.m4:37: AX_LIB_CURSES is expanded from... configure.in:43: the top level configure.in:46: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:46: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:46: the top level configure.in:93: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:43: TEA_PATH_TCLCONFIG is expanded from... configure.in:93: the top level configure.in:94: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:94: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:355: TEA_LOAD_TCLCONFIG is expanded from... configure.in:94: the top level configure.in:96: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:96: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:200: TEA_PATH_TKCONFIG is expanded from... configure.in:96: the top level configure.in:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... ac_stubs/tcl.m4:2704: TEA_TCL_EARLY_FLAG is expanded from... ac_stubs/tcl.m4:2717: TEA_TCL_EARLY_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:102: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:102: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... ac_stubs/tcl.m4:2751: TEA_TCL_64BIT_FLAGS is expanded from... ac_stubs/tcl.m4:1040: TEA_CONFIG_CFLAGS is expanded from... configure.in:102: the top level configure.in:148: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:148: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_tklib.m4:27: AX_LIB_TKLIB is expanded from... configure.in:148: the top level configure.in:149: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:149: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_iwidgets.m4:28: AX_LIB_IWIDGETS is expanded from... configure.in:149: the top level configure.in:150: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:150: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itcl.m4:26: AX_LIB_ITCL is expanded from... configure.in:150: the top level configure.in:151: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:151: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ac_stubs/ax_lib_itk.m4:26: AX_LIB_ITK is expanded from... configure.in:151: the top level autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_configure -- --enable-64bit \ --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu \ --with-itk=/usr/lib/tcltk/x86_64-linux-gnu ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-64bit --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu --with-itk=/usr/lib/tcltk/x86_64-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 8.11.1 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking for png.h... yes checking for staden-io_lib-config... no checking for io_lib-config... /usr/bin/io_lib-config checking if io_lib version >= 1.12.5... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking for ncurses.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes checking for pwd.h... yes checking for gcc option to enable large file support... none needed checking for declarations of fseeko and ftello... yes checking for library containing cos... -lm checking for popen... yes checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... no checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking for egrep -e... (cached) /usr/bin/grep -E checking if 64bit support is requested... yes checking if 64bit Sparc VIS support is requested... no checking if compiler supports visibility "hidden"... yes checking if rpath support is requested... yes checking system version... Linux-6.12.9+bpo-amd64 checking for ar... ar checking if compiler accepts -m64 flag... yes checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... using long checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include/tcl8.6 checking for Tcl private include files... Using srcdir found in tclConfig.sh: /usr/include/tcl8.6/tcl-private checking for Tk public headers... /usr/include/tcl8.6 checking for Tk private include files... Using srcdir found in tkConfig.sh: /usr/include/tcl8.6/tk-private checking tklib directory... yes (/usr/share/tcltk/tklib0.9) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/x86_64-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/x86_64-linux-gnu/itk3.4) configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/share/tcltk/tklib0.9 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/x86_64-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/x86_64-linux-gnu/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' cd Misc && make -f /build/reproducible-path/staden-2.0.0+b11/./Misc/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./Misc SUBDIR=Misc all cd trev && make -f /build/reproducible-path/staden-2.0.0+b11/./trev/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./trev SUBDIR=trev all cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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 primer3 && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts all cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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/Misc' 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/trev' make[2]: warning: -j12 forced in submake: resetting jobserver mode. 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/primer3' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[2]: warning: -j12 forced in submake: resetting jobserver mode. /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/./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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o crash.o -c crash.c /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o date.o -c date.c make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c /build/reproducible-path/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c Nothing to build for Pregap4. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shell.o -c shell.c Nothing to build for spin_emboss. Nothing to build for scripts. make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' Nothing to build for data. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o error.o -c error.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o -c dpal.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -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 mkdir -p /build/reproducible-path/staden-2.0.0+b11/lib 2>/dev/null gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c touch /build/reproducible-path/staden-2.0.0+b11/lib/.dir gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array.o -c array.c primer3_main.c: In function 'pr_safe_malloc': primer3_main.c:520:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro 'OOM_ERROR' 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o locks.o -c locks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c primer3_main.c: In function 'boulder_print_oligos': primer3_main.c:416:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 416 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:416:30: note: directive argument in the range [1, 2147483647] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:970, from primer3_main.c:7: In function 'sprintf', inlined from 'boulder_print_oligos' at primer3_main.c:416:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c primer3_main.c: In function 'main': primer3_main.c:234:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); | ^~ In function 'boulder_print_pairs', inlined from 'main' at primer3_main.c:109:3: primer3_main.c:234:30: note: directive argument in the range [1, 2147483646] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In function 'sprintf', inlined from 'boulder_print_pairs' at primer3_main.c:234:7, inlined from 'main' at primer3_main.c:109:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ parse_db.c: In function 'parse_entry': parse_db.c:234:66: warning: '%s' directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); | ^~ ~~~~ In file included from /usr/include/stdio.h:970, from parse_db.c:19: In function 'sprintf', inlined from 'parse_entry' at parse_db.c:234:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 33 and 8224 bytes into a destination of size 8192 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/Misc' cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi all cd alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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/tk_utils' make[2]: warning: -j12 forced in submake: resetting jobserver mode. 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/text_utils' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba all cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/g' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./alf -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j12 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o cli_arg.o -c cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./eba -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./eba -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./init_exp -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tclXkeylist.o -c tclXkeylist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./get_scf_field -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tclXutil.o -c tclXutil.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./abi -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_debug.o -c tcl_debug.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o misc.o -c misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o text_output.o -c text_output.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkRaster.o -c tkRaster.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./hetins -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o sheet.o -c sheet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c alfsplit.c: In function 'main': alfsplit.c:347:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 363 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function 'readIndexEntry': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkSheet.o -c tkSheet.c 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 -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkSheet_common.o -c tkSheet_common.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIcomment abiIO.o getABIcomment.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o trace_print.o -c trace_print.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o postscript.o -c postscript.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -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 get_scf_field get_scf_field.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o split.o -c split.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTrace.o -c tkTrace.c alfsplit.c: In function 'main': alfsplit.c:312:29: warning: '%s' directive writing up to 2559 bytes into a region of size 25 [-Wformat-overflow=] 312 | sprintf (fname,"%sALF",name[i]) ; | ^~ In file included from /usr/include/stdio.h:970, from alfsplit.c:30: In function 'sprintf', inlined from 'main' at alfsplit.c:312:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 2563 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from tkRaster.c:45: tkRaster.c: In function 'DrawEnvIndex': tkRaster.c:2266:62: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2266 | entryPtr = Tcl_FindHashEntry (&(RasterPtr->drawEnvTable), (char*)drawenvno); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ tkRaster.c: In function 'CreateDrawEnv': tkRaster.c:2353:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2353 | (char*) (RasterPtr->drawEnvCount), | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ tkRaster.c: In function 'DestroyDrawEnv': tkRaster.c:2381:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2381 | (char*)(drawenvptr->index)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceComp.o -c tkTraceComp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceIO.o -c tkTraceIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tkTraceDisp.o -c tkTraceDisp.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o alfsplit alfsplit.o -lm gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o capture.o -c capture.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o canvas_box.o -c canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o ruler_tick.o -c ruler_tick.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o restriction_enzyme_map.o -c restriction_enzyme_map.c capture.c: In function 'tcl_capture': capture.c:53:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | read(fd, buf, statbuf.st_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o element_canvas.o -c element_canvas.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o container.o -c container.c tkTraceDisp.c: In function 'trace_draw_numbers': tkTraceDisp.c:746:32: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 746 | sprintf(number, "%d", cind); | ^ In file included from /usr/include/stdio.h:970, from tkTraceDisp.c:2: In function 'sprintf', inlined from 'trace_draw_numbers' at tkTraceDisp.c:746:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o container_ruler.o -c container_ruler.c 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -o tcl_io_lib.o -c tcl_io_lib.c g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o hetins hetins.o -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/hetins' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -D_GNU_SOURCE -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' make[2]: warning: -j12 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss2.o -c align_ss2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_sv.o -c align_sv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dna_utils.o -c dna_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c sequence_formats.c: In function 'get_embl_format_seq': sequence_formats.c:729:29: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 729 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:33: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 738 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function 'add_feat': sequence_formats.c:481:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 481 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 510 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib.o -c align_lib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.c renz_utils.c: In function 'SetREnzColour': renz_utils.c:1049:35: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 1049 | sprintf(colour, "#%02x%02x%02x", r, g, b); | ^ In file included from /usr/include/stdio.h:970, from renz_utils.c:3: In function 'sprintf', inlined from 'SetREnzColour' at renz_utils.c:1049:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 26 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all cd spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin 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 vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip all cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./qclip SUBDIR=qclip all cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all 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 stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops all cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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/qclip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[2]: warning: -j12 forced in submake: resetting jobserver mode. g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./screen_seq -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./stops -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./vector_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./find_renz -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./qclip -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./make_weights -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./text_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o 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 -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_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 -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 raster_cmds.c: In function 'RasterResults': raster_cmds.c:250:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 250 | zoom = (int)gen.result; | ^ seq_raster.c: In function 'GetRasterZoom': seq_raster.c:1512:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1512 | result = (int)gen.result; | ^ seq_raster.c: In function 'seq_raster_callback': seq_raster.c:3012:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3012 | jdata->info.result = (void *)zoom; | ^ seq_raster.c:3034:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3034 | jdata->info.result = (void *)zoom; | ^ 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 -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqedInterface.o -c seqedInterface.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c 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; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -lm make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpam.o -c readpam.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/make_weights' emboss_input_funcs.c: In function 'read_emboss_data_file': emboss_input_funcs.c:402:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 402 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 444 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 477 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function 'init_emboss_stick_create': emboss_input_funcs.c:658:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 658 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 659 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/stops' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:316:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 316 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from /build/reproducible-path/staden-2.0.0+b11/./tk_utils/tkRaster.h:9, from seq_reg.h:6, from sequence_pair_display.c:4: In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:316:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequence_pair_display.c: In function 'update_seqs': sequence_pair_display.c:344:27: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 344 | sprintf(tmp, "%10d", i*10); | ^ In function 'sprintf', inlined from 'update_seqs' at sequence_pair_display.c:344:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sp_alignment.cpp: In function 'void sp::store_hashn(Hash*)': sp_alignment.cpp:754:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 754 | register int i,j,n; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_similar_spans.o -c sip_similar_spans.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o screen_seq screen_seq.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c sip_find_identity.c: In function 'identities_callback': sip_find_identity.c:210:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 210 | jdata->info.result = (void *)id; | ^ sip_align.c: In function 'align_callback': sip_align.c:181:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 181 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c sip_similar_spans.c: In function 'similar_spans_callback': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c sip_similar_spans.c:289:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 289 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp sip_quick_scan.c: In function 'quick_scan_callback': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c 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; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probs.o -c probs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c sip_sim.c: In function 'sim_callback': sip_sim.c:197:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 197 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c nip_base_comp.c: In function 'plot_base_comp_callback': nip_base_comp.c:183:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c nip_gene_search.c: In function 'plot_gene_search_callback': nip_gene_search.c:206:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 206 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 nip_stop_codon.c: In function 'nip_stop_codons_callback': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c nip_stop_codon.c:195:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 195 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c nip_splice_search.c: In function 'splice_search_callback': nip_splice_search.c:183:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c nip_string_search.c: In function 'nip_string_search_callback': nip_string_search.c:170:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 170 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp nip_wtmatrix_search.c: In function 'nip_wtmatrix_search_callback': nip_wtmatrix_search.c:167:38: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 167 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./spin -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libspin.so seq_reg.o seq_reg_cmds.o raster_cmds.o seq_raster.o sequtils.o seq_results.o seq_sendto.o spin_globals.o seq_plot_funcs.o seqed.o tkSeqed.o tkSeqedUtils.o tkSeqedNames.o seqed_write.o seqedInterface.o seqed_translate.o seqed_restriction_enzymes.o seqed_search.o sequence_pair_display.o emboss_input_funcs.o readpam.o compare_spans.o sip_hash.o sip_similar_spans.o sip_find_identity.o sip_quick_scan.o sip_align.o sip_globals.o sip_cmds.o sip_results.o rescan_matches.o probs.o sim.o sip_sim.o init.o nip_globals.o nip_cmds.o nip_base_comp.o nip_gene_search.o nip_trna_search.o codon_content.o nip_stop_codon.o trna_search.o splice_search.o nip_splice_search.o nip_string_search.o nip_wtmatrix_search.o nip_restriction_enzymes.o nip_canvas_box.o dinuc_freqs.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c make[2]: [/build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile:81: /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so align.o basecall.o caller.o caller_snr.o caller_base.o caller_level.o dnatable.o muttag.o mutationtag.o mutationtag_utils.o pathutil.o peakcall.o stringlist.o tagarray.o trace.o validate.o read_matrix.o sp_align_lib.o sp_alignment.o sp_hash_lib.o sp_matrix.o tracediff.o tracediff_helper.o tracediff_mutations.o tracediff_parameters.o tracediff_validate.o tracealign.o tracealign_cache.o tracealign_helper.o tracealign_interpolate.o tracealign_preprocess.o tracealign_validate.o mutscan.o mutscan_helper.o mutscan_validate.o mutscan_analysis.o mutscan_preprocess.o mutscan_parameters.o -lseq_utils -ltk_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm find_oligo.c: In function 'StringMatch': find_oligo.c:957:40: warning: '%ld' directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ find_oligo.c:957:41: note: format string is defined here 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); find_oligo.c:957:40: note: directive argument in the range [0, 9223372036854775807] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ In file included from /usr/include/stdio.h:970, from /build/reproducible-path/staden-2.0.0+b11/./gap5/hache_table.h:5, from /build/reproducible-path/staden-2.0.0+b11/./gap5/g-struct.h:24, from /build/reproducible-path/staden-2.0.0+b11/./gap5/g.h:1, from tg_struct.h:4, from tg_gio.h:4, from io_utils.h:6, from find_oligo.c:4: In function 'sprintf', inlined from 'StringMatch' at find_oligo.c:957:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 20 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[2]: warning: -j12 forced in submake: resetting jobserver mode. cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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/mutscan' 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]: warning: -j12 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./tracediff -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./mutscan -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c actf.c: In function 'actf_lock': actf.c:246:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 246 | write(fd, db_path, strlen(db_path)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c io_utils.c: In function 'template_name_to_number': io_utils.c:38:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 38 | return (int)Tcl_GetHashValue(hash); | ^ io_utils.c: In function 'read_name_to_number': io_utils.c:84:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 84 | return (int)Tcl_GetHashValue(hash); | ^ In file included from IO1.h:50, from io_utils.h:6, from io_utils.c:6: io_utils.c: In function 'cache_template_name': io_utils.c:549:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 549 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2556:64: note: in definition of macro 'Tcl_SetHashValue' 2556 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (void *)(value)) | ^~~~~ io_utils.c: In function 'cache_read_name': io_utils.c:566:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 566 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2556:64: note: in definition of macro 'Tcl_SetHashValue' 2556 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (void *)(value)) | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c 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) { | ^ g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c g++ -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm /usr/bin/ld: warning: libtk_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c tman_display.c: In function 'repositionSeq': tman_display.c:279:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:279:18: note: assuming directive output of 12 bytes 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: In function 'sprintf', inlined from 'repositionSeq' at tman_display.c:279:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c /usr/bin/ld: warning: libtk_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o preass.o -c preass.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list.o -c list.c make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probe.o -c probe.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template.o -c template.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash.o -c hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c readpair.c: In function 'readpair_obj_func': readpair.c:175:57: warning: '%s' directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", | ^~ 176 | *handle, c_list); | ~~~~~~ In file included from /usr/include/stdio.h:970, from readpair.c:18: In function 'sprintf', inlined from 'readpair_obj_func' at readpair.c:175:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 27 and 1060 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap5 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libgap5.so -L/build/reproducible-path/staden-2.0.0+b11/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c /usr/bin/ld: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c tg_index_common.o: in function `bttmp_file_open': ./gap5/./gap5/tg_index_common.c:105:(.text+0x5b2): 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clip.o -c clip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c copy_db.c: In function 'copy_read_name': copy_db.c:118:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 118 | sprintf(num, "#%d", iter++); | ^~ copy_db.c:118:30: note: directive argument in the range [1, 2147483646] 118 | sprintf(num, "#%d", iter++); | ^~~~~ In file included from /usr/include/stdio.h:970, from copy_db.c:1: In function 'sprintf', inlined from 'copy_read_name' at copy_db.c:118:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap5' consistency_display.c: In function 'consistency_join': consistency_display.c:160:22: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | gen.data = (void *)remove_dup; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c template_display.c: In function 'template_callback': template_display.c:2354:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from template_display.c:2: In function 'sprintf', inlined from 'template_callback' at template_display.c:2354:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ notes.c: In function 'time_t2str': notes.c:829:21: warning: ' (' directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 829 | sprintf(buf, "%s (%ld)", buf2, (long)t); | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from notes.c:11: In function 'sprintf', inlined from 'time_t2str' at notes.c:829:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1047 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c 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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c consistency_display.c: In function 'consistency_callback': consistency_display.c:883:50: warning: '%s' directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 883 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from consistency_display.c:1: In function 'sprintf', inlined from 'consistency_callback' at consistency_display.c:883:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 21 or more bytes (assuming 120) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c 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); | ^ strand_coverage.c: In function 'strand_coverage_callback': strand_coverage.c:503:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 503 | jdata->generic.data = (void *)scov->cons_id; | ^ strand_coverage.c:541:49: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 541 | strand_coverage_join(io, c, scov, (int)jdata->generic.data); | ^ 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); | ^ In file included from vseqs.c:3: vseqs.c: In function 'new_vcontig': vseqs.c:60:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 60 | hash = Tcl_CreateHashEntry(&db->num_hash, (char *)rnum, | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function 'new_vrseq': vseqs.c:158:51: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 158 | hash = Tcl_CreateHashEntry(&vc->num_hash, (char *)(vrseq->rnum), &new); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:62: note: in definition of macro 'Tcl_CreateHashEntry' 2573 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function 'del_vrseq': vseqs.c:215:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 215 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)(vrseq->rnum)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ vseqs.c: In function 'vrseq_index2ptr': vseqs.c:409:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 409 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)num); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2570:60: note: in definition of macro 'Tcl_FindHashEntry' 2570 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o undo.o -c undo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o join.o -c join.c tman_display.c: In function 'repositionSeq': tman_display.c:281:21: warning: ' xview moveto ' directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:125, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: In function 'sprintf', inlined from 'repositionSeq' at tman_display.c:281:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 28 and 2096 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c copy_db_main.c: In function 'main': copy_db_main.c:86:9: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.c gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o copy_db gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o copy_db.o copy_db_main.o text-io-reg.o io_utils.o io_handle.o -lg -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/. -I/build/reproducible-path/staden-2.0.0+b11/./mutlib -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libgap.so -L/build/reproducible-path/staden-2.0.0+b11/lib gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o IO2.o seqInfo.o parse_ft.o IO3.o io_utils.o io_handle.o gap-tcl.o tk-io-reg.o gap_cli_arg.o gap_globals.o newgap_cmds.o init.o consen.o gap_hash.o qual.o qualIO.o bubbl3.o tagdb.o notedb.o active_tags.o dbcheck.o clones.o extract.o preass.o list.o reactions.o probe.o template.o template_display.o ruler_display.o gap_canvas_box.o hash.o gap_array.o show_relationships.o fij.o hash_lib.o do_fij.o auto_assemble.o dis_readings.o find_repeats.o break_contig.o quality_plot.o readpair.o contig_selector.o complement.o cs-object.o list_proc.o dstrand.o oligo_sel.o primlib.o alter_rel.o restriction_enzymes.o stop_codon.o assemble_direct.o check_assembly.o tagU2.o mess.o find_oligo.o copy_db.o contig_order.o clip.o notes.o consistency_display.o consistency_canvas_box.o confidence_graph.o reading_coverage.o readpair_coverage.o strand_coverage.o find_fragments.o vseqs.o legacy_f2c.o f2c.o shuffle_pads.o auto_break.o tkEditor.o tkEdNames.o tkEdUtils.o edInterface.o edUtils2.o tagU1.o undo.o edExtend.o edCommands.o edMutations.o tagEditor.o searchUtils.o tman_interface.o tman_display.o tman_cons.o tman_diff.o contigEditor.o join.o oligo.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/gap4' cd copy_reads && make -f /build/reproducible-path/staden-2.0.0+b11/./copy_reads/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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 prefinish && make -f /build/reproducible-path/staden-2.0.0+b11/./prefinish/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd haplo && make -f /build/reproducible-path/staden-2.0.0+b11/./haplo/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3163303 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/haplo' make[2]: warning: -j12 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/convert' make[2]: warning: -j12 forced in submake: resetting jobserver mode. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish.o -c finish.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_filter.o -c finish_filter.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o process.o -c process.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./convert -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c main.c: In function 'get_db': main.c:87:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.c copy_reads.c: In function 'create_si_struct': copy_reads.c:125:26: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 125 | sprintf(comment, "%s %s", tag_text, io_name(io)); | ^~ In file included from /usr/include/stdio.h:970, from copy_reads.c:4: In function 'sprintf', inlined from 'create_si_struct' at copy_reads.c:125:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm copy_reads.c: In function 'copy_reads': copy_reads.c:409:34: warning: '%s' directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); | ^~ In function 'sprintf', inlined from 'copy_reads' at copy_reads.c:409:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz /usr/bin/ld: warning: libtext_utils.so, needed by /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./copy_reads -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -llzma -lbz2 -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap gcc -shared -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./haplo -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/reproducible-path/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' 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/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 -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-2.0.0+b11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m64 -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/reproducible-path/staden-2.0.0+b11/./prefinish -I/build/reproducible-path/staden-2.0.0+b11/./Misc -I/build/reproducible-path/staden-2.0.0+b11/./gap4 -I/build/reproducible-path/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/reproducible-path/staden-2.0.0+b11/./tk_utils -I/build/reproducible-path/staden-2.0.0+b11/./seq_utils -I/build/reproducible-path/staden-2.0.0+b11/./primer3/src -I/build/reproducible-path/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/reproducible-path/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/reproducible-path/staden-2.0.0+b11/lib/libprefinish.so finish.o finish_hash.o finish_long.o finish_main.o finish_utils.o finish_walk.o finish_reverse.o finish_filter.o finish_pcr.o dust.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/doc mkdir -p /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/man cp shlib.conf /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp ./staden.profile /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' cd Misc && make -f /build/reproducible-path/staden-2.0.0+b11/./Misc/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./Misc SUBDIR=Misc install cd trev && make -f /build/reproducible-path/staden-2.0.0+b11/./trev/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./trev SUBDIR=trev install cd primer3 && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 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. cd primer3/src && make -f /build/reproducible-path/staden-2.0.0+b11/./primer3/src/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 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/trev' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd pregap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install cd spin_emboss && make -f /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install cd scripts && make -f /build/reproducible-path/staden-2.0.0+b11/./scripts/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./scripts SUBDIR=scripts install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd data && make -f /build/reproducible-path/staden-2.0.0+b11/./data/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./data SUBDIR=data install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/scripts' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: warning: -j12 forced in submake: resetting jobserver mode. install trev /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libmisc.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden /build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev /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/lib/libprimer3.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/Misc' install pregap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 make[4]: Nothing to be done for 'install'. mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3' cp /build/reproducible-path/staden-2.0.0+b11/./scripts/assemble4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/reproducible-path/staden-2.0.0+b11/./trev/trev.tcl /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/primer3/src' cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss 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 mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 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 cp /build/reproducible-path/staden-2.0.0+b11/./data/alus/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cd tk_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./tk_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install cd text_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./text_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install cd abi && make -f /build/reproducible-path/staden-2.0.0+b11/./abi/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./abi SUBDIR=abi install 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. 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/./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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/trev' cd alf && make -f /build/reproducible-path/staden-2.0.0+b11/./alf/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 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. 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 cd g && make -f /build/reproducible-path/staden-2.0.0+b11/./g/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./g SUBDIR=g install cp /build/reproducible-path/staden-2.0.0+b11/./scripts/splitseq_da /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cd eba && make -f /build/reproducible-path/staden-2.0.0+b11/./eba/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./eba SUBDIR=eba install cd init_exp && make -f /build/reproducible-path/staden-2.0.0+b11/./init_exp/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/g' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/alf' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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 cp /build/reproducible-path/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd get_scf_field && make -f /build/reproducible-path/staden-2.0.0+b11/./get_scf_field/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/eba' 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/pregap4/templates make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/scripts' cp getABISampleName getABIcomment getABIdate getABIfield /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libtk_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/lib/libtext_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes 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. 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/./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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/text_utils' cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd hetins && make -f /build/reproducible-path/staden-2.0.0+b11/./hetins/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./hetins SUBDIR=hetins install mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp alfsplit /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp eba /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libg.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/abi' cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/*.tcl /build/reproducible-path/staden-2.0.0+b11/./tk_utils/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin_emboss' make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/hetins' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/./data/blast_data/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/eba' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/alf' cp init_exp /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp get_scf_field /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/g' 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 make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/init_exp' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/get_scf_field' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp: cannot stat '/build/reproducible-path/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory make[4]: [/build/reproducible-path/staden-2.0.0+b11/./pregap4/Makefile:42: install] Error 1 (ignored) cp /build/reproducible-path/staden-2.0.0+b11/./pregap4/naming_schemes/*.p4t /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/reproducible-path/staden-2.0.0+b11/./tk_utils/stash /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./data/gcodes/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp hetins /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin 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/./pregap4/pregap4rc /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/hetins' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tk_utils' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/pregap4' 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 cd seq_utils && make -f /build/reproducible-path/staden-2.0.0+b11/./seq_utils/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/./data/RENZYM.* /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 cp /build/reproducible-path/staden-2.0.0+b11/lib/libseq_utils.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/./data/vector_primer /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./data/pam250 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/reproducible-path/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/data' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/reproducible-path/staden-2.0.0+b11/./mutlib/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutlib SUBDIR=mutlib install cd spin && make -f /build/reproducible-path/staden-2.0.0+b11/./spin/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./spin SUBDIR=spin install cd vector_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./vector_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install cd screen_seq && make -f /build/reproducible-path/staden-2.0.0+b11/./screen_seq/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/spin' make[4]: warning: -j12 forced in submake: resetting jobserver mode. 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/vector_clip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd qclip && make -f /build/reproducible-path/staden-2.0.0+b11/./qclip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 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. cd polyA_clip && make -f /build/reproducible-path/staden-2.0.0+b11/./polyA_clip/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install cd stops && make -f /build/reproducible-path/staden-2.0.0+b11/./stops/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./stops SUBDIR=stops install cd make_weights && make -f /build/reproducible-path/staden-2.0.0+b11/./make_weights/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cd find_renz && make -f /build/reproducible-path/staden-2.0.0+b11/./find_renz/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/stops' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' cd gap5 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap5/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap5' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp vector_clip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libmutlib.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install spin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp screen_seq /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/vector_clip' cp polyA_clip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp qclip /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp make_weights /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/screen_seq' mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/polyA_clip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/qclip' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutlib' cp stops /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp find_renz /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./spin/*.tcl /build/reproducible-path/staden-2.0.0+b11/./spin/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/make_weights' cd gap4 && make -f /build/reproducible-path/staden-2.0.0+b11/./gap4/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/find_renz' cd tracediff && make -f /build/reproducible-path/staden-2.0.0+b11/./tracediff/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 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' cd mutscan && make -f /build/reproducible-path/staden-2.0.0+b11/./mutscan/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/gap4' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[4]: warning: -j12 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[4]: warning: -j12 forced in submake: resetting jobserver mode. cp /build/reproducible-path/staden-2.0.0+b11/lib/libspin.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install gap5 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp /build/reproducible-path/staden-2.0.0+b11/./spin/*.wts /build/reproducible-path/staden-2.0.0+b11/./spin/niprc /build/reproducible-path/staden-2.0.0+b11/./spin/siprc /build/reproducible-path/staden-2.0.0+b11/./spin/spinrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./gap5/*.tcl /build/reproducible-path/staden-2.0.0+b11/./gap5/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp tracediff /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp mutscan /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/tracediff' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/mutscan' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/spin' cp /build/reproducible-path/staden-2.0.0+b11/./gap5/../gap4/acd2tag.tcl /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp copy_db /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./gap5/gap5rc /build/reproducible-path/staden-2.0.0+b11/./gap5/gap5rc_menu_full /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc install gap4 /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libgap5.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp /build/reproducible-path/staden-2.0.0+b11/./gap4/*.tcl /build/reproducible-path/staden-2.0.0+b11/./gap4/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp tg_index.bin /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin install tg_index /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/lib/libgap.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install gap5_cmd /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' 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 -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install cd haplo && make -f /build/reproducible-path/staden-2.0.0+b11/./haplo/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./haplo SUBDIR=haplo install cd copy_reads && make -f /build/reproducible-path/staden-2.0.0+b11/./copy_reads/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install cd convert && make -f /build/reproducible-path/staden-2.0.0+b11/./convert/Makefile -j12 --jobserver-auth=fifo:/tmp/GMfifo3167605 BUILD=/build/reproducible-path/staden-2.0.0+b11 SRC=/build/reproducible-path/staden-2.0.0+b11/./convert SUBDIR=convert install make[4]: Entering directory '/build/reproducible-path/staden-2.0.0+b11/haplo' make[4]: warning: -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. 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/copy_reads mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp staden_convert /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo install copy_reads /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.tcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itcl /build/reproducible-path/staden-2.0.0+b11/./prefinish/*.itk /build/reproducible-path/staden-2.0.0+b11/./prefinish/help /build/reproducible-path/staden-2.0.0+b11/./prefinish/args.template /build/reproducible-path/staden-2.0.0+b11/./prefinish/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/convert' cp /build/reproducible-path/staden-2.0.0+b11/./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/./copy_reads/copy_reads.tcl /build/reproducible-path/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/reproducible-path/staden-2.0.0+b11/./copy_reads/tclIndex /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads cp /build/reproducible-path/staden-2.0.0+b11/lib/libcopy_reads.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/lib/libhaplo.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/reproducible-path/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/config.prefinish /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/reproducible-path/staden-2.0.0+b11/./haplo/haplorc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/reproducible-path/staden-2.0.0+b11/lib/libprefinish.so /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/copy_reads' make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/haplo' install prefinish /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_sanger /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_cDNA /build/reproducible-path/staden-2.0.0+b11/./prefinish/finish_cDNA_ends_only \ /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/rules/*.rule /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/reproducible-path/staden-2.0.0+b11/./prefinish/config.prefinish /build/reproducible-path/staden-2.0.0+b11/./prefinish/prefinishrc /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11/prefinish' make[3]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' make[2]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' # Remove file causing lintian errors that is targeting at windows find debian -name help_windows.tcl -delete # Remove some empty directories find debian -type d -empty -name acdtcl -delete find debian -type d -empty -name templates -delete # Build system is not prepared for multi-arch mv /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/* /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/reproducible-path/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_install dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_installman -Nstaden dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/reproducible-path/staden-2.0.0+b11' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-5_amd64.deb'. dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-5_amd64.deb'. dpkg-deb: building package 'staden-common' in '../staden-common_2.0.0+b11-5_all.deb'. dpkg-genbuildinfo --build=binary -O../staden_2.0.0+b11-5_amd64.buildinfo dpkg-genchanges --build=binary -O../staden_2.0.0+b11-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3146679 and its subdirectories I: Current time: Wed Mar 11 07:35:44 -12 2026 I: pbuilder-time-stamp: 1773257744