Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/tigr-glimmer/tigr-glimmer_3.02b-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/tigr-glimmer-3.02b-5cdx7ona4/tigr-glimmer_3.02b-5_amd64.buildinfo Get source package info: tigr-glimmer=3.02b-5 Source URL: http://snapshot.notset.fr/mr/package/tigr-glimmer/3.02b-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34-6 binutils-common=2.34-6 binutils-x86-64-linux-gnu=2.34-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.35.1-5 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-12 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.8.0-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 file=1:5.38-4 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-12 gcc=4:9.2.1-3.1 gcc-10-base=10.1.0-1 gcc-9=9.3.0-12 gcc-9-base=9.3.0-12 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan5=9.3.0-12 libatomic1=10.1.0-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34-6 libblkid1=2.35.1-5 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-8 libc-dev-bin=2.30-8 libc6=2.30-8 libc6-dev=2.30-8 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10.1.0-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34-6 libctf0=2.34-6 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.252 libdebhelper-perl=13 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libgcc-9-dev=9.3.0-12 libgcc-s1=10.1.0-1 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.2-1 libgmp10=2:6.2.0+dfsg-4 libgomp1=10.1.0-1 libgpg-error0=1.37-1 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10.1.0-1 liblsan0=10.1.0-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.35.1-5 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-10 libpipeline1=1.5.2-2 libquadmath0=10.1.0-1 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.35.1-5 libstdc++-9-dev=9.3.0-12 libstdc++6=10.1.0-1 libsub-override-perl=0.09-2 libsystemd0=245.5-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.1.0-1 libubsan1=10.1.0-1 libuchardet0=0.0.6-3 libudev1=245.5-2 libunistring2=0.9.10-2 libuuid1=2.35.1-5 libxml2=2.9.10+dfsg-5 linux-libc-dev=5.6.7-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-2+b1 man-db=2.9.1-1 mawk=1.3.4.20200120-2 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.0-10 perl-base=5.30.0-10 perl-modules-5.30=5.30.0-10 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 util-linux=2.35.1-5 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200514T144953Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d tigr-glimmer=3.02b-5 && mkdir -p /build/tigr-glimmer-VT9oZu && dpkg-source --no-check -x /*.dsc /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b && chown -R builduser:builduser /build/tigr-glimmer-VT9oZu" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1589401196" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/tigr-glimmer-VT9oZu /tmp/tigr-glimmer-3.02b-5cdx7ona4 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200514T144953Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.7FQAkkb0vz as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.7FQAkkb0vz Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.1-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200514T144953Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200514T144953Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (1093 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4482 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-8) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200514T144953Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.7FQAkkb0vz Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200514T144953Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1146 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.7FQAkkb0vz I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d tigr-glimmer=3.02b-5 && mkdir -p /build/tigr-glimmer-VT9oZu && dpkg-source --no-check -x /*.dsc /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b && chown -R builduser:builduser /build/tigr-glimmer-VT9oZu"' exec /tmp/mmdebstrap.7FQAkkb0vz Reading package lists... NOTICE: 'tigr-glimmer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tigr-glimmer.git Please use: git clone https://salsa.debian.org/med-team/tigr-glimmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5660 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tigr-glimmer 3.02b-5 (dsc) [2060 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tigr-glimmer 3.02b-5 (tar) [5638 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tigr-glimmer 3.02b-5 (diff) [20.2 kB] Fetched 5660 kB in 5s (1244 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'tigr-glimmer_3.02b-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting tigr-glimmer in /build/tigr-glimmer-VT9oZu/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: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1589401196" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.7FQAkkb0vz 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 amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b' dh_clean cd src; make clean make[2]: Entering directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src' cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; rm -f cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib; rm -f cd /build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common clean ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; rm -f delcher.o fasta.o gene.o cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib; rm -f libGLMcommon.a cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin; rm -f rm -f delcher.d fasta.d gene.d make[3]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM clean ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; rm -f icm.o build-icm.o build-fixed.o score-fixed.o cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib; rm -f libGLMicm.a cd /build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer clean ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; rm -f anomaly.o glimmer3.o long-orfs.o test.o cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib; rm -f cd /build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util clean ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/lib; rm -f cd /build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src' rm -f bin/* lib/* obj/* make[1]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b' dh_auto_build --sourcedirectory=src -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd src && make -j4 "INSTALL=install --strip-program=true" "CFLAGS=-g -O2 -fdebug-prefix-map=/build/tigr-glimmer-VT9oZu/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-VT9oZu/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-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/delcher.o delcher.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/fasta.o fasta.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/gene.o gene.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ ################### libGLMcommon.a ##################### cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj && \ ar rvs /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a delcher.o fasta.o gene.o ar: creating /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a a - delcher.o a - fasta.o a - gene.o make[3]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/icm.o icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ 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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/build-icm.o build-icm.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/build-fixed.o build-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/score-fixed.o score-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/obj && \ ar rvs /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMicm.a icm.o build-icm.o build-fixed.o score-fixed.o ar: creating /build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-icm -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-icm; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ build-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "build-fixed.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/build-fixed; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ score-fixed ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "score-fixed.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/score-fixed -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ -lGLMicm \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/score-fixed; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/anomaly.o anomaly.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/glimmer3.o glimmer3.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ @@@@@@@@@@@@@@@@@@@ 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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/long-orfs.o long-orfs.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/test.o test.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/anomaly -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/anomaly; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ glimmer3 ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "glimmer3.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/glimmer3 -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMicm.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/glimmer3; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ long-orfs ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "long-orfs.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/long-orfs -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/long-orfs; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ test ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "test.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/test -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/test; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/entropy-profile.o entropy-profile.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/entropy-score.o entropy-score.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/extract.o extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/multi-extract.o multi-extract.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/start-codon-distrib.o start-codon-distrib.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/uncovered.o uncovered.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b=. -fstack-protector-strong -Wformat -Werror=format-security -c \ -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -I/../SYS/inc -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Common -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util -I/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/inc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj/window-acgt.o window-acgt.cc ; \ else \ /cm/cmtools/bin/links.pl /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj \ " :/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-profile -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-profile; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ entropy-score ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "entropy-score.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-score -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/entropy-score; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "extract.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ multi-extract ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "multi-extract.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/multi-extract -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/multi-extract; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "start-codon-distrib.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/start-codon-distrib -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/start-codon-distrib; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ uncovered ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "uncovered.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/uncovered -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/uncovered; \ exit ${STATUS}; \ fi; \ fi ; ++++++++++++++++++++ window-acgt ++++++++++++++++++++++ set -e ; \ STATUS=0 ; \ if [ -z "window-acgt.o" ] ; then \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ cc -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ else \ cd /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/obj; \ g++ -o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/window-acgt -Wl,-z,relro -Wl,-z,now \ -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/lib/libGLMcommon.a \ \ || STATUS=${?} ; \ if [ ${STATUS} != 0 ] ; then \ rm -f /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/bin/window-acgt; \ exit ${STATUS}; \ fi; \ fi ; make[3]: Leaving directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Common' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/ICM all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/ICM' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Glimmer all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Glimmer' ##### Making Directory /build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src/Util all ##### make[3]: Entering directory '/build/tigr-glimmer-VT9oZu/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-VT9oZu/tigr-glimmer-3.02b/src/Util' make[2]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b/src' make[1]: Leaving directory '/build/tigr-glimmer-VT9oZu/tigr-glimmer-3.02b' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'tigr-glimmer-dbgsym' in '../tigr-glimmer-dbgsym_3.02b-5_amd64.deb'. dpkg-deb: building package 'tigr-glimmer' in '../tigr-glimmer_3.02b-5_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tigr-glimmer_3.02b-5_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/tigr-glimmer-VT9oZu /tmp/tigr-glimmer-3.02b-5cdx7ona4 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.7FQAkkb0vz... I: success in 304.5552 seconds md5: tigr-glimmer-dbgsym_3.02b-5_amd64.deb: OK md5: tigr-glimmer_3.02b-5_amd64.deb: OK sha1: tigr-glimmer-dbgsym_3.02b-5_amd64.deb: OK sha1: tigr-glimmer_3.02b-5_amd64.deb: OK sha256: tigr-glimmer-dbgsym_3.02b-5_amd64.deb: OK sha256: tigr-glimmer_3.02b-5_amd64.deb: OK Checksums: OK