Sun Aug 15 06:02:23 UTC 2021 I: starting to build tigr-glimmer/bullseye/armhf on jenkins on '2021-08-15 06:02' Sun Aug 15 06:02:23 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_5/2011/console.log Sun Aug 15 06:02:23 UTC 2021 I: Downloading source for bullseye/tigr-glimmer=3.02b-5 --2021-08-15 06:02:24-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tigr-glimmer/tigr-glimmer_3.02b-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2060 (2.0K) Saving to: ‘tigr-glimmer_3.02b-5.dsc’ 0K .. 100% 150M=0s 2021-08-15 06:02:24 (150 MB/s) - ‘tigr-glimmer_3.02b-5.dsc’ saved [2060/2060] Sun Aug 15 06:02:24 UTC 2021 I: tigr-glimmer_3.02b-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tigr-glimmer Binary: tigr-glimmer Architecture: any Version: 3.02b-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://ccb.jhu.edu/software/glimmer/index.shtml Standards-Version: 4.5.0 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 (= 12) Package-List: tigr-glimmer deb science optional arch=any Checksums-Sha1: 665ed5c676c6d495e4354893e67ee605ec3e00da 5637975 tigr-glimmer_3.02b.orig.tar.gz 69ad0825e3f5620d96802e0de1288bea04c3339e 20212 tigr-glimmer_3.02b-5.debian.tar.xz Checksums-Sha256: ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 5637975 tigr-glimmer_3.02b.orig.tar.gz 5781e3cfe06ab4fd639813b6de9014b91becdb9dd2ff4a97b0d6bf3c817a83e9 20212 tigr-glimmer_3.02b-5.debian.tar.xz Files: 344d012ae12596de905866fe9eb7f16c 5637975 tigr-glimmer_3.02b.orig.tar.gz ecacd45fca39436ae36feb90da416c9e 20212 tigr-glimmer_3.02b-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl686AARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEUsQ/+JLrCD2WzTMqnQyadM37aXrfjkQpMP2vq ySi5eNC8HI5Y9OMJwTsVSHwXSWwospMMxD1DEuBxdGaYbKnoQ3R73uB68huwPGca IXHnKb8H4B68HVRy6n2MTA7H81jZg1oYZuMc2XPDmZXauIZUsrqcfxw0klAKTorZ uhH15kstH8ZTbL+eMXH+cBVP57yuuEhJumE3Gfe2YrL/0A6fVDDjby3nkDrg76YF 4JtUnAcgvXbPPIl8WwbxD3B3MrS+zTTBqdafPC5WY/1v1/ZetJS4TfbE6ViP0YJK qJGDfy8k04R4o5F81bfVOfFWVwsqFGWfZQ80Xa2VNm8IgpTdSbV/GQKPpSyJgktu 9cfvLvTgx8XQKa2+lHXLoWFGZTVVLMDt2x53qWQCxgWrkl+ME099mXQLob78jTme F6hO6dATIVx1HbrL572S0rjXyyPQRb5RRr2+wP8zbYPKxifxGW+pYMw+NQkIAUNb QU4h2opUsaMHHbAuT4lzVyjUp/BXXTGWigrNFDEQRLP56m9AxDn45EDOonlnbxlW bC4I1uuRJqMUNNkZFM9gKbAkjIHe9ieo58LsRptc+0rC95KGenXd8FtkTKY6P1b9 hgroWnq5KR++xQ1ZM1oax/Yw5i4/w3FPc92ZaqwQwWCFPFE8D6iSVStLGeJxl1bO cxtGSwt6L0E= =UU8Y -----END PGP SIGNATURE----- Sun Aug 15 06:02:24 UTC 2021 I: Checking whether the package is not for us Sun Aug 15 06:02:24 UTC 2021 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Sun Aug 15 06:02:24 UTC 2021 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Sun Aug 15 06:10:26 UTC 2021 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 14 18:02:33 -12 2021 I: pbuilder-time-stamp: 1629007353 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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-5.dsc] I: copying [./tigr-glimmer_3.02b.orig.tar.gz] I: copying [./tigr-glimmer_3.02b-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.NUV3g4IS/trustedkeys.kbx': General error gpgv: Signature made Wed May 13 18:41:04 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tigr-glimmer_3.02b-5.dsc 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-5.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/20086/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c856c6086f6d4281ac23ed4d3d168fa3' 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='20086' 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/tmp.yovSw5q2jH/pbuilderrc_243X --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/b1 --logfile b1/build.log tigr-glimmer_3.02b-5.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt64a 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 12 21:28 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/20086/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 (= 12) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 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 (= 12); 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 17.7 MB of archives. After unpacking 62.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Fetched 17.7 MB in 5s (3903 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... 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Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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/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-5_source.changes dpkg-buildpackage: info: source package tigr-glimmer dpkg-buildpackage: info: source version 3.02b-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Etienne 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/tigr-glimmer-3.02b' dh_clean cd src; make clean make[2]: Entering directory '/build/tigr-glimmer-3.02b/src' cd /build/tigr-glimmer-3.02b/obj; rm -f cd /build/tigr-glimmer-3.02b/lib; rm -f cd /build/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/tigr-glimmer-3.02b/src/Common clean ##### make[3]: Entering directory '/build/tigr-glimmer-3.02b/src/Common' if [ -e gene.cc ] ; then \ /bin/sh -ec 'g++ -M -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; cd /build/tigr-glimmer-3.02b/obj; rm -f delcher.o fasta.o gene.o cd /build/tigr-glimmer-3.02b/lib; rm -f libGLMcommon.a cd /build/tigr-glimmer-3.02b/bin; rm -f rm -f delcher.d fasta.d gene.d make[3]: Leaving directory '/build/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-3.02b/src/ICM clean ##### make[3]: Entering directory '/build/tigr-glimmer-3.02b/src/ICM' if [ -e score-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; cd /build/tigr-glimmer-3.02b/obj; rm -f icm.o build-icm.o build-fixed.o score-fixed.o cd /build/tigr-glimmer-3.02b/lib; rm -f libGLMicm.a cd /build/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/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-3.02b/src/Glimmer clean ##### make[3]: Entering directory '/build/tigr-glimmer-3.02b/src/Glimmer' if [ -e test.cc ] ; then \ /bin/sh -ec 'g++ -M -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; cd /build/tigr-glimmer-3.02b/obj; rm -f anomaly.o glimmer3.o long-orfs.o test.o cd /build/tigr-glimmer-3.02b/lib; rm -f cd /build/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/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-3.02b/src/Util clean ##### make[3]: Entering directory '/build/tigr-glimmer-3.02b/src/Util' if [ -e window-acgt.cc ] ; then \ /bin/sh -ec 'g++ -M -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc entropy-profile.cc \ | sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \ fi ; cd /build/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/tigr-glimmer-3.02b/lib; rm -f cd /build/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/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/tigr-glimmer-3.02b/src' rm -f bin/* lib/* obj/* make[1]: Leaving directory '/build/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/tigr-glimmer-3.02b' dh_auto_build --sourcedirectory=src -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd src && make -j3 "INSTALL=install --strip-program=true" "CFLAGS=-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/delcher.o delcher.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" delcher.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ fasta.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e fasta.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/fasta.o fasta.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" fasta.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ gene.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e gene.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/gene.o gene.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" gene.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from delcher.hh:32, from gene.cc:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = DNA_vect_t; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from delcher.hh:32, from gene.cc:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'bool PWM_t::Read(FILE*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'PWM_t& PWM_t::operator=(const PWM_t&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ################### libGLMcommon.a ##################### cd /build/tigr-glimmer-3.02b/obj && \ ar rvs /build/tigr-glimmer-3.02b/lib/libGLMcommon.a delcher.o fasta.o gene.o ar: creating /build/tigr-glimmer-3.02b/lib/libGLMcommon.a a - delcher.o a - fasta.o a - gene.o make[3]: Leaving directory '/build/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/icm.o icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" icm.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from icm.hh:15, from icm.cc:16: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from icm.hh:15, from icm.cc:16: /usr/include/c++/10/bits/stl_vector.h: In member function 'void ICM_t::Cumulative_Score(const string&, std::vector&, int) const': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ build-icm.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e build-icm.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/build-icm.o build-icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" build-icm.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ build-fixed.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e build-fixed.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/build-fixed.o build-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" build-fixed.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ score-fixed.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e score-fixed.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/score-fixed.o score-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" score-fixed.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition ################### libGLMicm.a ##################### cd /build/tigr-glimmer-3.02b/obj && \ ar rvs /build/tigr-glimmer-3.02b/lib/libGLMicm.a icm.o build-icm.o build-fixed.o score-fixed.o ar: creating /build/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/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ build-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "build-fixed.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ score-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "score-fixed.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/anomaly.o anomaly.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" anomaly.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ glimmer3.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e glimmer3.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/glimmer3.o glimmer3.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" glimmer3.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition 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++/10/vector:72, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_vector.h: In function 'void Integerize_Scores(std::vector, int, std::vector, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_vector.h: In function 'void Parse_Command_Line(int, char**)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Start_t; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Gene_t; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_vector.h: In function 'void Set_Start_And_Stop_Codons()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'void Score_Orflist(FILE*, FILE*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:25, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:25, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:25, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:32, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from /build/tigr-glimmer-3.02b/src/Common/delcher.hh:25, from glimmer3.hh:15, from glimmer3.cc:17: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ long-orfs.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e long-orfs.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/long-orfs.o long-orfs.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" long-orfs.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/test.o test.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" test.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition ++++++++++++++++++++ anomaly ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "anomaly.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ glimmer3 ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "glimmer3.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ long-orfs ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "long-orfs.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ test ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "test.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/entropy-profile.o entropy-profile.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" entropy-profile.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e entropy-score.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/entropy-score.o entropy-score.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" entropy-score.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/extract.o extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" extract.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ multi-extract.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e multi-extract.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/multi-extract.o multi-extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" multi-extract.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ start-codon-distrib.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e start-codon-distrib.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/start-codon-distrib.o start-codon-distrib.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" start-codon-distrib.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ uncovered.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e uncovered.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/uncovered.o uncovered.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" uncovered.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ window-acgt.cc @@@@@@@@@@@@@@@@@@@@@ set -e ; \ if [ -e window-acgt.cc ] ; then \ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__cplusplus -g -O2 -fdebug-prefix-map=/build/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-3.02b/obj/window-acgt.o window-acgt.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-3.02b/obj" window-acgt.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition ++++++++++++++++++++ entropy-profile ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "entropy-profile.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ entropy-score ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "entropy-score.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "extract.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ multi-extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "multi-extract.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "start-codon-distrib.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ uncovered ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "uncovered.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ window-acgt ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "window-acgt.o" ] ; then \ cd /build/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/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/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/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/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/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/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/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/tigr-glimmer-3.02b/src' make[1]: Leaving directory '/build/tigr-glimmer-3.02b' create-stamp debian/debhelper-build-stamp dh_prep 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 dh_strip dh_makeshlibs dh_shlibdeps 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/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/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/uncovered 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/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/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/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/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/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/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/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-icm 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-dbgsym' in '../tigr-glimmer-dbgsym_3.02b-5_armhf.deb'. dpkg-deb: building package 'tigr-glimmer' in '../tigr-glimmer_3.02b-5_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tigr-glimmer_3.02b-5_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/20086 and its subdirectories I: Current time: Sat Aug 14 18:10:19 -12 2021 I: pbuilder-time-stamp: 1629007819 Sun Aug 15 06:10:28 UTC 2021 I: 1st build successful. Starting 2nd build on remote node cbxi4b-armhf-rb.debian.net. Sun Aug 15 06:10:28 UTC 2021 I: Preparing to do remote build '2' on cbxi4b-armhf-rb.debian.net. Sun Aug 15 06:31:12 UTC 2021 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net. Sun Aug 15 06:31:14 UTC 2021 I: tigr-glimmer_3.02b-5_armhf.changes: Format: 1.8 Date: Wed, 13 May 2020 22:19:56 +0200 Source: tigr-glimmer Binary: tigr-glimmer tigr-glimmer-dbgsym Architecture: armhf Version: 3.02b-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Etienne Mollier Description: tigr-glimmer - Gene detection in archea and bacteria Closes: 960294 Changes: tigr-glimmer (3.02b-5) unstable; urgency=medium . * Team upload. * Reinforce Makefile error checking and increase verbosity; initial version for 3.02b-4 missed at least one point at linking time. Closes: #960294 Checksums-Sha1: 14fbc0e94b6766a6fc9cb480b636019ea9a15a22 1325824 tigr-glimmer-dbgsym_3.02b-5_armhf.deb 316bd2ef50eca43ba7a6cf5444ac488d7c963046 4796 tigr-glimmer_3.02b-5_armhf.buildinfo c4dd9691bc8403c3bbe57281c5a134c38eb2a67a 262484 tigr-glimmer_3.02b-5_armhf.deb Checksums-Sha256: c3f28417ae9a8343904c705d0a2cea10ef01a6441cd8e52843a051877f8ede5a 1325824 tigr-glimmer-dbgsym_3.02b-5_armhf.deb eae6a43829fcd2dabc5990646b223b715e67ce936fe69d5fa5eb05902dfdaa20 4796 tigr-glimmer_3.02b-5_armhf.buildinfo bcf9cfed74e8f49cd6793daabe7eb1752a369ac9e709be832cebdbb51742ff4b 262484 tigr-glimmer_3.02b-5_armhf.deb Files: 7d39537ac5e7f39cdda1093db074b62b 1325824 debug optional tigr-glimmer-dbgsym_3.02b-5_armhf.deb ce38159cf86d0b8d9af3849e28189430 4796 science optional tigr-glimmer_3.02b-5_armhf.buildinfo 876bd3f963999759ce0d4fc383b9b152 262484 science optional tigr-glimmer_3.02b-5_armhf.deb Sun Aug 15 06:31:15 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/tigr-glimmer_3.02b-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/tigr-glimmer_3.02b-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/tigr-glimmer_3.02b-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/b1/tigr-glimmer_3.02b-5_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.yovSw5q2jH/b2/tigr-glimmer_3.02b-5_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: 0.515s) 0.515s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.061s) 0.061s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Aug 15 06:31:18 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Aug 15 06:31:18 UTC 2021 I: tigr-glimmer from bullseye built successfully and reproducibly on armhf. Sun Aug 15 06:31:20 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Aug 15 06:31:20 UTC 2021 I: Submitting 8.0K b1/tigr-glimmer_3.02b-5_armhf.buildinfo.asc Sun Aug 15 06:31:21 UTC 2021 I: Submitting 8.0K b2/tigr-glimmer_3.02b-5_armhf.buildinfo.asc Sun Aug 15 06:31:22 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Aug 15 06:31:22 UTC 2021 I: Done submitting .buildinfo files. Sun Aug 15 06:31:22 UTC 2021 I: Removing signed tigr-glimmer_3.02b-5_armhf.buildinfo.asc files: removed './b1/tigr-glimmer_3.02b-5_armhf.buildinfo.asc' removed './b2/tigr-glimmer_3.02b-5_armhf.buildinfo.asc'