Sat May 4 06:58:37 UTC 2024 I: starting to build tigr-glimmer/trixie/armhf on jenkins on '2024-05-04 06:58' Sat May 4 06:58:37 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_26/4098/console.log Sat May 4 06:58:37 UTC 2024 I: Downloading source for trixie/tigr-glimmer=3.02b-6 --2024-05-04 06:58:37-- http://deb.debian.org/debian/pool/main/t/tigr-glimmer/tigr-glimmer_3.02b-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2104 (2.1K) [text/prs.lines.tag] Saving to: ‘tigr-glimmer_3.02b-6.dsc’ 0K .. 100% 347M=0s 2024-05-04 06:58:37 (347 MB/s) - ‘tigr-glimmer_3.02b-6.dsc’ saved [2104/2104] Sat May 4 06:58:37 UTC 2024 I: tigr-glimmer_3.02b-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tigr-glimmer Binary: tigr-glimmer Architecture: any Version: 3.02b-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Étienne Mollier Homepage: http://ccb.jhu.edu/software/glimmer/index.shtml Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/tigr-glimmer Vcs-Git: https://salsa.debian.org/med-team/tigr-glimmer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: tigr-glimmer deb science optional arch=any Checksums-Sha1: 665ed5c676c6d495e4354893e67ee605ec3e00da 5637975 tigr-glimmer_3.02b.orig.tar.gz 409b805f26572654d9aa3a6acacbaa047ffbd0f3 20516 tigr-glimmer_3.02b-6.debian.tar.xz Checksums-Sha256: ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 5637975 tigr-glimmer_3.02b.orig.tar.gz 94d8f00b7052a4792cd9612f9ef91eb229194f3dbaf057794c98112805b5537f 20516 tigr-glimmer_3.02b-6.debian.tar.xz Files: 344d012ae12596de905866fe9eb7f16c 5637975 tigr-glimmer_3.02b.orig.tar.gz b743ca043f6fd888e7892afd584d113b 20516 tigr-glimmer_3.02b-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmFrHLAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoe1g/8DNy6wTJQhG6eKP+/bWm/eXg9hrEm 5cAJrxl8P6WzA6qnCS1402E46hW2r/bRGG11y8R10Rf/kgRWprsd1utdIQdG7wez ru3W1Q7h6sPP3jbr5wd0/DotCOGc3tGsO1HNZmiiklKm2o3Jvzqypb5YX5cbib5C shHbC1mEqOugcthKlcbJchueAt5ZwPVoOkm9FuzJayaYAiQf52LSlmoJTJVETZOZ Ftn31Fi1WMtI6WhtHbCG4cNj581d4RyaKkuD6V6vg0gEOJOn0rAIwc8TscsgCd0K pZ702LNWf50e1a1ZeSjOB1IcHmh4tPMetvnfcjp6GWbAVejhSnRkPo6tzlFs7mqt aKiCvajVsmQPfiIKe9SV+f7KAYU6X34n6tGlHRot9N4jfNSO0Wpp0HeU7+q22N1m nHmP4cOaJFDNzF4KEEWxVPWDn19HEmv/jjLCq0UVfYlMx+uFuV6NxR6XEHyFtRTD 4VFU9dM9c9JMw+i46z+8DWwkSxpEfQS17nUziN6MxbTQwqPcD9JT8nL89oGyUBqw H25vwIXp7dYvVh0eW4Mi/dyNDI7ssvkWYSuNBxzovAYk25v0x9VO2HA9eS9secBR 3nsDIDVkCAF0ezKnsvchcRToPN6I4YetSaV+4crRL2dptCvV6YEtdABbxyK5PhnL 0cQRN3hIlW2punY= =Ep2R -----END PGP SIGNATURE----- Sat May 4 06:58:37 UTC 2024 I: Checking whether the package is not for us Sat May 4 06:58:37 UTC 2024 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net. Sat May 4 06:58:37 UTC 2024 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net. Sat May 4 07:00:31 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 3 18:58:43 -12 2024 I: pbuilder-time-stamp: 1714805923 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tigr-glimmer_3.02b-6.dsc] I: copying [./tigr-glimmer_3.02b.orig.tar.gz] I: copying [./tigr-glimmer_3.02b-6.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Oct 16 18:40:48 2021 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tigr-glimmer_3.02b-6.dsc: no acceptable signature found dpkg-source: info: extracting tigr-glimmer in tigr-glimmer-3.02b dpkg-source: info: unpacking tigr-glimmer_3.02b.orig.tar.gz dpkg-source: info: unpacking tigr-glimmer_3.02b-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_gcc4.3.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying make-errs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17812/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='e6bbb139616748ea969b7d6b2a67c033' 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='17812' 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.Mzt1bRWO/pbuilderrc_QVZV --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/b1 --logfile b1/build.log tigr-glimmer_3.02b-6.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64z 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 2 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17812/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: armhf 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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19441 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After unpacking 68.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Fetched 18.4 MB in 0s (96.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19441 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../22-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-19) ... 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/tigr-glimmer-3.02b/ && 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 > ../tigr-glimmer_3.02b-6_source.changes dpkg-buildpackage: info: source package tigr-glimmer dpkg-buildpackage: info: source version 3.02b-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b' dh_clean cd src; make clean make[2]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src' cd /build/reproducible-path/tigr-glimmer-3.02b/obj; rm -f cd /build/reproducible-path/tigr-glimmer-3.02b/lib; rm -f cd /build/reproducible-path/tigr-glimmer-3.02b/bin; rm -f rm -f echo "* Make Target is " clean; * Make Target is clean set -e ; for i in Common ICM Glimmer Util; do if [ -d $i ]; then cd $i; echo "##### Making Directory " `pwd` " " clean " #####"; make clean; cd ..; fi; done; ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Common clean ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' if [ -e gene.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc gene.cc \ | sed '\''s/gene\\.o[ :]*/& gene.d/g'\'' > gene.d' ; \ fi ; if [ -e fasta.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc fasta.cc \ | sed '\''s/fasta\\.o[ :]*/& fasta.d/g'\'' > fasta.d' ; \ fi ; if [ -e delcher.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; cd /build/reproducible-path/tigr-glimmer-3.02b/obj; rm -f delcher.o fasta.o gene.o cd /build/reproducible-path/tigr-glimmer-3.02b/lib; rm -f libGLMcommon.a cd /build/reproducible-path/tigr-glimmer-3.02b/bin; rm -f rm -f delcher.d fasta.d gene.d make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/ICM clean ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' if [ -e score-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc score-fixed.cc \ | sed '\''s/score-fixed\\.o[ :]*/& score-fixed.d/g'\'' > score-fixed.d' ; \ fi ; if [ -e build-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc build-fixed.cc \ | sed '\''s/build-fixed\\.o[ :]*/& build-fixed.d/g'\'' > build-fixed.d' ; \ fi ; if [ -e build-icm.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc build-icm.cc \ | sed '\''s/build-icm\\.o[ :]*/& build-icm.d/g'\'' > build-icm.d' ; \ fi ; if [ -e icm.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; cd /build/reproducible-path/tigr-glimmer-3.02b/obj; rm -f icm.o build-icm.o build-fixed.o score-fixed.o cd /build/reproducible-path/tigr-glimmer-3.02b/lib; rm -f libGLMicm.a cd /build/reproducible-path/tigr-glimmer-3.02b/bin; rm -f build-icm build-fixed score-fixed rm -f icm.d build-icm.d build-fixed.d score-fixed.d make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer clean ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' if [ -e test.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc test.cc \ | sed '\''s/test\\.o[ :]*/& test.d/g'\'' > test.d' ; \ fi ; if [ -e long-orfs.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc long-orfs.cc \ | sed '\''s/long-orfs\\.o[ :]*/& long-orfs.d/g'\'' > long-orfs.d' ; \ fi ; if [ -e glimmer3.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc glimmer3.cc \ | sed '\''s/glimmer3\\.o[ :]*/& glimmer3.d/g'\'' > glimmer3.d' ; \ fi ; if [ -e anomaly.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; cd /build/reproducible-path/tigr-glimmer-3.02b/obj; rm -f anomaly.o glimmer3.o long-orfs.o test.o cd /build/reproducible-path/tigr-glimmer-3.02b/lib; rm -f cd /build/reproducible-path/tigr-glimmer-3.02b/bin; rm -f anomaly glimmer3 long-orfs test rm -f anomaly.d glimmer3.d long-orfs.d test.d make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Util clean ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' if [ -e window-acgt.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc window-acgt.cc \ | sed '\''s/window-acgt\\.o[ :]*/& window-acgt.d/g'\'' > window-acgt.d' ; \ fi ; if [ -e uncovered.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc uncovered.cc \ | sed '\''s/uncovered\\.o[ :]*/& uncovered.d/g'\'' > uncovered.d' ; \ fi ; if [ -e start-codon-distrib.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc start-codon-distrib.cc \ | sed '\''s/start-codon-distrib\\.o[ :]*/& start-codon-distrib.d/g'\'' > start-codon-distrib.d' ; \ fi ; if [ -e multi-extract.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc multi-extract.cc \ | sed '\''s/multi-extract\\.o[ :]*/& multi-extract.d/g'\'' > multi-extract.d' ; \ fi ; if [ -e extract.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc extract.cc \ | sed '\''s/extract\\.o[ :]*/& extract.d/g'\'' > extract.d' ; \ fi ; if [ -e entropy-score.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc entropy-score.cc \ | sed '\''s/entropy-score\\.o[ :]*/& entropy-score.d/g'\'' > entropy-score.d' ; \ fi ; if [ -e entropy-profile.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc entropy-profile.cc \ | sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \ fi ; cd /build/reproducible-path/tigr-glimmer-3.02b/obj; rm -f entropy-profile.o entropy-score.o extract.o multi-extract.o start-codon-distrib.o uncovered.o window-acgt.o cd /build/reproducible-path/tigr-glimmer-3.02b/lib; rm -f cd /build/reproducible-path/tigr-glimmer-3.02b/bin; rm -f entropy-profile entropy-score extract multi-extract start-codon-distrib uncovered window-acgt rm -f entropy-profile.d entropy-score.d extract.d multi-extract.d start-codon-distrib.d uncovered.d window-acgt.d make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src' rm -f bin/* lib/* obj/* make[1]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b' dh_auto_build --sourcedirectory=src -- CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" CPPFLAGS="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd src && make -j3 "INSTALL=install --strip-program=true" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src' TGT=objs echo "* Make Target is " all; * Make Target is all set -e ; for i in Common ICM Glimmer Util; do if [ -d $i ]; then cd $i; echo "##### Making Directory " `pwd` " " all " #####"; make all; cd ..; fi; done; ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. if [ -e gene.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc gene.cc \ | sed '\''s/gene\\.o[ :]*/& gene.d/g'\'' > gene.d' ; \ fi ; if [ -e fasta.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc fasta.cc \ | sed '\''s/fasta\\.o[ :]*/& fasta.d/g'\'' > fasta.d' ; \ fi ; if [ -e delcher.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e delcher.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/delcher.o delcher.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" delcher.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ fasta.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e fasta.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/fasta.o fasta.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" fasta.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ gene.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e gene.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/gene.o gene.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" gene.o ; \ fi ; gene.cc: In member function 'bool PWM_t::Read(FILE*)': gene.cc:319:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 319 | fscanf (fp, "%d", & width); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ gene.cc:332:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 332 | fscanf (fp, "%s", tag); // skip tag in first column | ~~~~~~~^~~~~~~~~~~~~~~ gene.cc:335:17: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fscanf (fp, "%lf", & x); | ~~~~~~~^~~~~~~~~~~~~~~~ gene.cc: In function 'int Read_String(FILE*, char*&, long int&, char*, int)': gene.cc:848:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets (Line, MAX_LINE, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ ################### libGLMcommon.a ##################### cd /build/reproducible-path/tigr-glimmer-3.02b/obj && \ ar rvs /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a delcher.o fasta.o gene.o ar: creating /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a a - delcher.o a - fasta.o a - gene.o make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. if [ -e score-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc score-fixed.cc \ | sed '\''s/score-fixed\\.o[ :]*/& score-fixed.d/g'\'' > score-fixed.d' ; \ fi ; if [ -e build-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc build-fixed.cc \ | sed '\''s/build-fixed\\.o[ :]*/& build-fixed.d/g'\'' > build-fixed.d' ; \ fi ; if [ -e build-icm.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc build-icm.cc \ | sed '\''s/build-icm\\.o[ :]*/& build-icm.d/g'\'' > build-icm.d' ; \ fi ; if [ -e icm.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e icm.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/icm.o icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" icm.o ; \ fi ; icm.cc: In member function 'void Fixed_Length_ICM_t::read(const char*)': icm.cc:1491:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1491 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ icm.cc:1519:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1519 | fread (permutation, sizeof (int), length, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ build-icm.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e build-icm.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/build-icm.o build-icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" build-icm.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ build-fixed.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e build-fixed.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/build-fixed.o build-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" build-fixed.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ score-fixed.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e score-fixed.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/score-fixed.o score-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" score-fixed.o ; \ fi ; ################### libGLMicm.a ##################### cd /build/reproducible-path/tigr-glimmer-3.02b/obj && \ ar rvs /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMicm.a icm.o build-icm.o build-fixed.o score-fixed.o ar: creating /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMicm.a a - icm.o a - build-icm.o a - build-fixed.o a - score-fixed.o ++++++++++++++++++++ build-icm ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "build-icm.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ build-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "build-fixed.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ score-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "score-fixed.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. if [ -e test.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc test.cc \ | sed '\''s/test\\.o[ :]*/& test.d/g'\'' > test.d' ; \ fi ; if [ -e long-orfs.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc long-orfs.cc \ | sed '\''s/long-orfs\\.o[ :]*/& long-orfs.d/g'\'' > long-orfs.d' ; \ fi ; if [ -e glimmer3.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc glimmer3.cc \ | sed '\''s/glimmer3\\.o[ :]*/& glimmer3.d/g'\'' > glimmer3.d' ; \ fi ; if [ -e anomaly.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e anomaly.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/anomaly.o anomaly.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" anomaly.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ glimmer3.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e glimmer3.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/glimmer3.o glimmer3.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" glimmer3.o ; \ fi ; glimmer3.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': glimmer3.cc:2607:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2607 | fgets (line, MAX_LINE, fp); // skip header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Start_t&}; _Tp = Start_t; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Gene_t&}; _Tp = Gene_t; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void Parse_Command_Line(int, char**)' at glimmer3.cc:1793:36: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Set_Start_And_Stop_Codons()' at glimmer3.cc:3258:38: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void Set_Start_And_Stop_Codons()' at glimmer3.cc:3271:34: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/tigr-glimmer-3.02b/src/Common/delcher.hh:25: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Gene_t; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Start_t; _Alloc = std::allocator]', inlined from 'void Score_Orfs(std::vector&, std::vector&, FILE*)' at glimmer3.cc:2934:38, inlined from 'int main(int, char**)' at glimmer3.cc:252:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Gene_t; _Alloc = std::allocator]', inlined from 'void Score_Orfs(std::vector&, std::vector&, FILE*)' at glimmer3.cc:3020:34, inlined from 'int main(int, char**)' at glimmer3.cc:252:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Gene_t; _Alloc = std::allocator]', inlined from 'void Trace_Back(FILE*, const Event_Node_t&)' at glimmer3.cc:3424:34, inlined from 'int main(int, char**)' at glimmer3.cc:262:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Gene_t; _Alloc = std::allocator]', inlined from 'void Trace_Back(FILE*, const Event_Node_t&)' at glimmer3.cc:3443:34, inlined from 'int main(int, char**)' at glimmer3.cc:262:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const Gene_t&, const Gene_t&)]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void Trace_Back(FILE*, const Event_Node_t&)' at glimmer3.cc:3472:9, inlined from 'int main(int, char**)' at glimmer3.cc:262:21: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const Gene_t&, const Gene_t&)]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void Trace_Back(FILE*, const Event_Node_t&)' at glimmer3.cc:3472:9, inlined from 'int main(int, char**)' at glimmer3.cc:262:21: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ long-orfs.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e long-orfs.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/long-orfs.o long-orfs.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" long-orfs.o ; \ fi ; long-orfs.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': long-orfs.cc:1317:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1317 | fgets (line, MAX_LINE, fp); // skip header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ test.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e test.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/test.o test.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" test.o ; \ fi ; ++++++++++++++++++++ anomaly ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "anomaly.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ glimmer3 ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "glimmer3.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ long-orfs ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "long-orfs.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ test ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "test.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. if [ -e window-acgt.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc window-acgt.cc \ | sed '\''s/window-acgt\\.o[ :]*/& window-acgt.d/g'\'' > window-acgt.d' ; \ fi ; if [ -e uncovered.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc uncovered.cc \ | sed '\''s/uncovered\\.o[ :]*/& uncovered.d/g'\'' > uncovered.d' ; \ fi ; if [ -e start-codon-distrib.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc start-codon-distrib.cc \ | sed '\''s/start-codon-distrib\\.o[ :]*/& start-codon-distrib.d/g'\'' > start-codon-distrib.d' ; \ fi ; if [ -e multi-extract.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc multi-extract.cc \ | sed '\''s/multi-extract\\.o[ :]*/& multi-extract.d/g'\'' > multi-extract.d' ; \ fi ; if [ -e extract.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc extract.cc \ | sed '\''s/extract\\.o[ :]*/& extract.d/g'\'' > extract.d' ; \ fi ; if [ -e entropy-score.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc entropy-score.cc \ | sed '\''s/entropy-score\\.o[ :]*/& entropy-score.d/g'\'' > entropy-score.d' ; \ fi ; if [ -e entropy-profile.cc ] ; then \ /bin/sh -ec 'g++ -M -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc entropy-profile.cc \ | sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \ fi ; make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e entropy-profile.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/entropy-profile.o entropy-profile.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" entropy-profile.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e entropy-score.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/entropy-score.o entropy-score.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" entropy-score.o ; \ fi ; entropy-score.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': entropy-score.cc:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 327 | fgets (line, MAX_LINE, fp); // skip header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ extract.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e extract.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/extract.o extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" extract.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ multi-extract.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e multi-extract.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/multi-extract.o multi-extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" multi-extract.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ start-codon-distrib.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e start-codon-distrib.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/start-codon-distrib.o start-codon-distrib.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" start-codon-distrib.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ uncovered.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e uncovered.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/uncovered.o uncovered.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" uncovered.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ window-acgt.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e window-acgt.cc ] ; then \ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/tigr-glimmer-3.02b=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c \ -I/build/reproducible-path/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/reproducible-path/tigr-glimmer-3.02b/src/Common -I/build/reproducible-path/tigr-glimmer-3.02b/src/ICM -I/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer -I/build/reproducible-path/tigr-glimmer-3.02b/src/Util -I/build/reproducible-path/tigr-glimmer-3.02b/inc -o /build/reproducible-path/tigr-glimmer-3.02b/obj/window-acgt.o window-acgt.cc ; \ else \ /cm/cmtools/bin/links.pl /build/reproducible-path/tigr-glimmer-3.02b/obj \ " :/build/reproducible-path/tigr-glimmer-3.02b/obj" window-acgt.o ; \ fi ; ++++++++++++++++++++ entropy-profile ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "entropy-profile.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ entropy-score ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "entropy-score.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "extract.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ multi-extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "multi-extract.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "start-codon-distrib.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ uncovered ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "uncovered.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ window-acgt ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "window-acgt.o" ] ; then \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ cc -o /build/reproducible-path/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ else \ cd /build/reproducible-path/tigr-glimmer-3.02b/obj; \ g++ -o /build/reproducible-path/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/build/reproducible-path/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/reproducible-path/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/reproducible-path/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' TGT=libs echo "* Make Target is " all; * Make Target is all set -e ; for i in Common ICM Glimmer Util; do if [ -d $i ]; then cd $i; echo "##### Making Directory " `pwd` " " all " #####"; make all; cd ..; fi; done; ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' TGT=progs echo "* Make Target is " all; * Make Target is all set -e ; for i in Common ICM Glimmer Util; do if [ -d $i ]; then cd $i; echo "##### Making Directory " `pwd` " " all " #####"; make all; cd ..; fi; done; ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/reproducible-path/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b/src' make[1]: Leaving directory '/build/reproducible-path/tigr-glimmer-3.02b' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tigr-glimmer/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/glimmer3 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/multi-extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/entropy-score contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/start-codon-distrib contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/build-icm contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/anomaly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/long-orfs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/score-fixed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/build-fixed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/window-acgt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/entropy-profile contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tigr-glimmer/usr/lib/tigr-glimmer/uncovered contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'tigr-glimmer' in '../tigr-glimmer_3.02b-6_armhf.deb'. dpkg-deb: building package 'tigr-glimmer-dbgsym' in '../tigr-glimmer-dbgsym_3.02b-6_armhf.deb'. dpkg-genbuildinfo --build=binary -O../tigr-glimmer_3.02b-6_armhf.buildinfo dpkg-genchanges --build=binary -O../tigr-glimmer_3.02b-6_armhf.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/17812 and its subdirectories I: Current time: Fri May 3 19:00:25 -12 2024 I: pbuilder-time-stamp: 1714806025 Sat May 4 07:00:34 UTC 2024 I: 1st build successful. Starting 2nd build on remote node cbxi4b-armhf-rb.debian.net. Sat May 4 07:00:34 UTC 2024 I: Preparing to do remote build '2' on cbxi4b-armhf-rb.debian.net. Sat May 4 07:07:04 UTC 2024 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net. Sat May 4 07:07:07 UTC 2024 I: tigr-glimmer_3.02b-6_armhf.changes: Format: 1.8 Date: Sat, 16 Oct 2021 20:37:42 +0200 Source: tigr-glimmer Binary: tigr-glimmer tigr-glimmer-dbgsym Architecture: armhf Version: 3.02b-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: tigr-glimmer - Gene detection in archea and bacteria Closes: 984367 Changes: tigr-glimmer (3.02b-6) unstable; urgency=medium . * d/rules: prevent CXXDEFS from setting __cplusplus (Closes: #984367) * d/control: add myself to uploaders * d/watch: fall back to http protocol to repair scan * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) Checksums-Sha1: 22fd83c099fbc7f66b0181b38f074d956a4db34c 1344108 tigr-glimmer-dbgsym_3.02b-6_armhf.deb b52070fd5fc38712c3a0b76de69af3319b03b565 5001 tigr-glimmer_3.02b-6_armhf.buildinfo 19d94e2d774219f190865816ac4014fd5a154fea 259456 tigr-glimmer_3.02b-6_armhf.deb Checksums-Sha256: eb9011cc26657fefe4ea5c6e55b6fa6b8f6fa0dce39f3aaf4345217b31539811 1344108 tigr-glimmer-dbgsym_3.02b-6_armhf.deb 393f0746789c3546f6807707101ce549f1d46c53beb5498beeb827a588f8f7b6 5001 tigr-glimmer_3.02b-6_armhf.buildinfo 4288b8930ae03a093b5e3b805b133ec91dff2827de9dcdea8cbda5af54120584 259456 tigr-glimmer_3.02b-6_armhf.deb Files: 43bc3f5b6402a2a96dbd724b183ceab9 1344108 debug optional tigr-glimmer-dbgsym_3.02b-6_armhf.deb 3c60e7af29683384a28557f33e5c8e65 5001 science optional tigr-glimmer_3.02b-6_armhf.buildinfo bd292356fecd18874fd0ce5b912bf911 259456 science optional tigr-glimmer_3.02b-6_armhf.deb Sat May 4 07:07:08 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_26-4098.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/tigr-glimmer_3.02b-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/tigr-glimmer_3.02b-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/tigr-glimmer_3.02b-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/b1/tigr-glimmer_3.02b-6_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.Mzt1bRWO/b2/tigr-glimmer_3.02b-6_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.389s) 0.389s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 743ms CPU time consumed: 742ms Sat May 4 07:07:09 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat May 4 07:07:09 UTC 2024 I: tigr-glimmer from trixie built successfully and reproducibly on armhf. Sat May 4 07:07:11 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 4 07:07:11 UTC 2024 I: Submitting 8.0K b1/tigr-glimmer_3.02b-6_armhf.buildinfo.asc Sat May 4 07:07:11 UTC 2024 I: Submitting 8.0K b2/tigr-glimmer_3.02b-6_armhf.buildinfo.asc Sat May 4 07:07:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 4 07:07:12 UTC 2024 I: Done submitting .buildinfo files. Sat May 4 07:07:12 UTC 2024 I: Removing signed tigr-glimmer_3.02b-6_armhf.buildinfo.asc files: removed './b1/tigr-glimmer_3.02b-6_armhf.buildinfo.asc' removed './b2/tigr-glimmer_3.02b-6_armhf.buildinfo.asc'