Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/subread/subread_2.0.3+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/subread-2.0.3+dfsg-1skin24gy/subread_2.0.3+dfsg-1_amd64.buildinfo Get source package info: subread=2.0.3+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/subread/2.0.3+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.51 bash=5.1-3+b1 bc=1.07.1-2+b2 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-8 bsdutils=1:2.36.1-8 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-8 libbz2-1.0=1.0.8-4 libc-bin=2.31-13 libc-dev-bin=2.31-13 libc6=2.31-13 libc6-dev=2.31-13 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-2 libcrypt-dev=1:4.4.18-5 libcrypt1=1:4.4.18-5 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.3.4 libdpkg-perl=1.20.9 libelf1=0.183-3 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-6 libicu67=67.1-7 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 liblsan0=10.2.1-6 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-8 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libreadline8=8.1-2 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.36.1-8 libsqlite3-0=3.34.1-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-6 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-6 libunistring2=0.9.10-4 libuuid1=2.36.1-8 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 python3=3.9.2-3 python3-minimal=3.9.2-3 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 readline-common=8.1-2 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-8 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=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/20210817T204926Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210817T204926Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210815T144423Z/ 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 subread=2.0.3+dfsg-1 && mkdir -p /build/subread-CRk9SD && dpkg-source --no-check -x /*.dsc /build/subread-CRk9SD/subread-2.0.3+dfsg && chown -R builduser:builduser /build/subread-CRk9SD" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/subread-CRk9SD/subread-2.0.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629029865" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/subread-CRk9SD /tmp/subread-2.0.3+dfsg-1skin24gy bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210815T144423Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.BwYfkkVSsK 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.BwYfkkVSsK Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-8). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210815T144423Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210815T144423Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (925 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 ... 4668 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-13) ... 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/20210817T204926Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210817T204926Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210815T144423Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.BwYfkkVSsK Get:1 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm InRelease [94.4 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210815T144423Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main Sources [11.5 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main amd64 Packages [11.2 MB] Fetched 22.8 MB in 19s (1217 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.BwYfkkVSsK I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d subread=2.0.3+dfsg-1 && mkdir -p /build/subread-CRk9SD && dpkg-source --no-check -x /*.dsc /build/subread-CRk9SD/subread-2.0.3+dfsg && chown -R builduser:builduser /build/subread-CRk9SD"' exec /tmp/mmdebstrap.BwYfkkVSsK Reading package lists... NOTICE: 'subread' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/subread.git Please use: git clone https://salsa.debian.org/med-team/subread.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.8 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main subread 2.0.3+dfsg-1 (dsc) [2313 B] Get:2 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main subread 2.0.3+dfsg-1 (tar) [13.8 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210817T204926Z bookworm/main subread 2.0.3+dfsg-1 (diff) [18.7 kB] Fetched 13.8 MB in 11s (1281 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'subread_2.0.3+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting subread in /build/subread-CRk9SD/subread-2.0.3+dfsg dpkg-source: info: unpacking subread_2.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_2.0.3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying cross.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/subread-CRk9SD/subread-2.0.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629029865" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.BwYfkkVSsK dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=makefile debian/rules override_dh_auto_clean make[1]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' dh_auto_clean rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux cd src && make -j10 clean -f Makefile.Linux make[2]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src' make[1]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' dh_autoreconf_clean -O--buildsystem=makefile dh_clean -O--buildsystem=makefile rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --buildsystem=makefile dh_update_autotools_config -a -O--buildsystem=makefile dh_autoreconf -a -O--buildsystem=makefile dh_auto_configure -a -O--buildsystem=makefile debian/rules override_dh_auto_build make[1]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \ cd src && make -j10 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc make[2]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src' x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM’: sambam-file.c:2381:24: warning: variable ‘last_written_BAI_chro’ set but not used [-Wunused-but-set-variable] 2381 | int old_chro_no = -1, last_written_BAI_chro = -1;; | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gene-algorithms.c: In function ‘miltime’: gene-algorithms.c:1585:3: warning: ‘ftime’ is deprecated [-Wdeprecated-declarations] 1585 | ftime(&trp); | ^~~~~ In file included from gene-algorithms.c:33: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c input-blc.c: In function ‘cacheBCL_qualTest_BAMmode’: input-blc.c:953:53: warning: variable ‘lane_str’ set but not used [-Wunused-but-set-variable] 953 | char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; | ^~~~~~~~ input-blc.c:953:31: warning: variable ‘sample_barcode’ set but not used [-Wunused-but-set-variable] 953 | char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version rm -f longread-one/*.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm make[3]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src/longread-one' x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:6105:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6105 | fread(§ion1_items,1, 8, input_fps[xk1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6108:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6108 | fread(&cellbcP0_geneno0B,1,8,input_fps[xk1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6109:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6109 | fread(&umis,1,8,input_fps[xk1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6130:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6130 | fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ global_context -> scRNA_UMI_length + 4, input_fps[xk1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6132:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6132 | fread(last_rbin_buffer[xk1] + 16+ 8*genes+ global_context -> scRNA_UMI_length + 4, 1, binlen, input_fps[xk1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6190:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6190 | fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ global_context -> scRNA_UMI_length + 4, input_fps[selected_fp_no]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6193:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6193 | fread(last_rbin_buffer[selected_fp_no] + 16+ 8*genes+ global_context -> scRNA_UMI_length + 4, 1, binlen, input_fps[selected_fp_no]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6240:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6240 | fread(&binlen, 1, 4, notmapped_fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:6243:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6243 | fread(tofill -> inbin + tofill -> inbin_len, 1, binlen, notmapped_fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c: In function ‘load_global_context_forindel’: SUBindel.c:66:24: warning: ‘.reads’ directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); | ^~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1006 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:77:25: warning: ‘.00.b.tab’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 77 | sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:75:25: warning: ‘.00.c.tab’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 75 | sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:87:26: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 1018 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:87:26: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 1018 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c: In function ‘load_indexes_forindel’: SUBindel.c:110:26: warning: ‘%02d’ directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ SUBindel.c:110:22: note: directive argument in the range [0, 2147483647] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 12 and 1019 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-CRk9SD/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE longread-mapping.c: In function ‘LRMmiltime’: longread-mapping.c:234:2: warning: ‘ftime’ is deprecated [-Wdeprecated-declarations] 234 | ftime(&trp); | ^~~~~ In file included from longread-mapping.c:33: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ make[3]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities ########################################################### # # # Installation successfully completed. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg/src' make[1]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=makefile dh_prep -a -O--buildsystem=makefile rm -f -- debian/subread.substvars rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/ rm -f debian/subread.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' find /build/subread-CRk9SD/subread-2.0.3+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; dh_auto_install install -d /build/subread-CRk9SD/subread-2.0.3\+dfsg/debian/tmp make[1]: Leaving directory '/build/subread-CRk9SD/subread-2.0.3+dfsg' dh_install -a -O--buildsystem=makefile install -d debian/subread/usr/bin cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/ install -d debian/subread/usr/lib/subread cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/genRandomReads ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/ install -d debian/.debhelper/generated/subread install -d debian/.debhelper/generated/subread-data dh_installdocs -a -O--buildsystem=makefile install -d debian/subread/usr/share/doc/subread cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread chmod -R u\+rw,go=rX debian/subread/usr/share/doc install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright dh_installchangelogs -a -O--buildsystem=makefile install -p -m0644 debian/changelog debian/subread/usr/share/doc/subread/changelog.Debian dh_installman -a -O--buildsystem=makefile install -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/exactSNP.1 debian/subread/usr/share/man/man1/exactSNP.1 install -p -m0644 ./debian/featureCounts.1 debian/subread/usr/share/man/man1/featureCounts.1 install -p -m0644 ./debian/flattenGTF.1 debian/subread/usr/share/man/man1/flattenGTF.1 install -p -m0644 ./debian/genRandomReads.1 debian/subread/usr/share/man/man1/genRandomReads.1 install -p -m0644 ./debian/propmapped.1 debian/subread/usr/share/man/man1/propmapped.1 install -p -m0644 ./debian/qualityScores.1 debian/subread/usr/share/man/man1/qualityScores.1 install -p -m0644 ./debian/removeDup.1 debian/subread/usr/share/man/man1/removeDup.1 install -p -m0644 ./debian/repair.1 debian/subread/usr/share/man/man1/repair.1 install -p -m0644 ./debian/subindel.1 debian/subread/usr/share/man/man1/subindel.1 install -p -m0644 ./debian/subjunc.1 debian/subread/usr/share/man/man1/subjunc.1 install -p -m0644 ./debian/sublong.1 debian/subread/usr/share/man/man1/sublong.1 install -p -m0644 ./debian/subread-align.1 debian/subread/usr/share/man/man1/subread-align.1 install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1 install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 dh_installinit -a -O--buildsystem=makefile dh_installsystemduser -a -O--buildsystem=makefile dh_perl -a -O--buildsystem=makefile dh_link -a -O--buildsystem=makefile dh_strip_nondeterminism -a -O--buildsystem=makefile dh_compress -a -O--buildsystem=makefile cd debian/subread chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 cd '/build/subread-CRk9SD/subread-2.0.3+dfsg' dh_fixperms -a -O--buildsystem=makefile find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -a -O--buildsystem=makefile dh_dwz -a -O--buildsystem=makefile install -d debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/202201d24ce350d32112666168a162396c5b6d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/202201d24ce350d32112666168a162396c5b6d.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/202201d24ce350d32112666168a162396c5b6d.debug debian/subread/usr/bin/exactSNP install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e8 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e8/28e640681af5a59eb109c490f5d83568b58f6d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e8/28e640681af5a59eb109c490f5d83568b58f6d.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e8/28e640681af5a59eb109c490f5d83568b58f6d.debug debian/subread/usr/bin/featureCounts install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9f3a0e514b318de12a41c858f61eb0405be6dd.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9f3a0e514b318de12a41c858f61eb0405be6dd.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9f3a0e514b318de12a41c858f61eb0405be6dd.debug debian/subread/usr/bin/subindel install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/05ab84fc7341265a6854aac55573fddc880966.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/05ab84fc7341265a6854aac55573fddc880966.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/05ab84fc7341265a6854aac55573fddc880966.debug debian/subread/usr/bin/subjunc install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9c/2b0188203a5bd93f9c10525f4bc10da97af256.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9c/2b0188203a5bd93f9c10525f4bc10da97af256.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9c/2b0188203a5bd93f9c10525f4bc10da97af256.debug debian/subread/usr/bin/sublong install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a2 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a2/d967075cc72b4d75b635845255b0fce1bef81f.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a2/d967075cc72b4d75b635845255b0fce1bef81f.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a2/d967075cc72b4d75b635845255b0fce1bef81f.debug debian/subread/usr/bin/subread-align install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9/78bc78251698d86dd9a9eb6cb1d31b7be5dc01.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9/78bc78251698d86dd9a9eb6cb1d31b7be5dc01.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9/78bc78251698d86dd9a9eb6cb1d31b7be5dc01.debug debian/subread/usr/bin/subread-buildindex install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6b/3448114b03c9f0af6b5d07f9b4b79f8dc018f9.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6b/3448114b03c9f0af6b5d07f9b4b79f8dc018f9.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6b/3448114b03c9f0af6b5d07f9b4b79f8dc018f9.debug debian/subread/usr/lib/subread/flattenGTF install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa/4602bf4fc1259dc08bdb65a78b49bdb66685aa.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa/4602bf4fc1259dc08bdb65a78b49bdb66685aa.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa/4602bf4fc1259dc08bdb65a78b49bdb66685aa.debug debian/subread/usr/lib/subread/genRandomReads install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/c9e978fa90ecfc09ea284fe228e10fcc96b3f0.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/c9e978fa90ecfc09ea284fe228e10fcc96b3f0.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/c9e978fa90ecfc09ea284fe228e10fcc96b3f0.debug debian/subread/usr/lib/subread/propmapped install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/16acb79aceb0297f1cf1ff96947e79f74a9e33.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/16acb79aceb0297f1cf1ff96947e79f74a9e33.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/16acb79aceb0297f1cf1ff96947e79f74a9e33.debug debian/subread/usr/lib/subread/qualityScores install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/338b853644f91abe47283bbb26ce1b03473908.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/338b853644f91abe47283bbb26ce1b03473908.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/338b853644f91abe47283bbb26ce1b03473908.debug debian/subread/usr/lib/subread/removeDup install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4/7b67d23e42ba76668414c853cc0f40ef3ee3b1.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4/7b67d23e42ba76668414c853cc0f40ef3ee3b1.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4/7b67d23e42ba76668414c853cc0f40ef3ee3b1.debug debian/subread/usr/lib/subread/repair install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7b/92e8dd30894d89b8d3098c71e683e7ec29f44c.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7b/92e8dd30894d89b8d3098c71e683e7ec29f44c.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7b/92e8dd30894d89b8d3098c71e683e7ec29f44c.debug debian/subread/usr/lib/subread/subread-fullscan install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/3d8620ecc54b9e8ca012b05802342c337aaf14.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/3d8620ecc54b9e8ca012b05802342c337aaf14.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/3d8620ecc54b9e8ca012b05802342c337aaf14.debug debian/subread/usr/lib/subread/txUnique install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug install -d debian/.debhelper/subread/dbgsym-root/usr/share/doc ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym dh_makeshlibs -a -O--buildsystem=makefile rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -d debian/subread/DEBIAN dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique dh_installdeb -a -O--buildsystem=makefile dh_gencontrol -a -O--buildsystem=makefile echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=163d8620ecc54b9e8ca012b05802342c337aaf14 41c9e978fa90ecfc09ea284fe228e10fcc96b3f0 6b3448114b03c9f0af6b5d07f9b4b79f8dc018f9 70202201d24ce350d32112666168a162396c5b6d 7b92e8dd30894d89b8d3098c71e683e7ec29f44c 7e05ab84fc7341265a6854aac55573fddc880966 9c2b0188203a5bd93f9c10525f4bc10da97af256 a2d967075cc72b4d75b635845255b0fce1bef81f a47b67d23e42ba76668414c853cc0f40ef3ee3b1 ac338b853644f91abe47283bbb26ce1b03473908 ae16acb79aceb0297f1cf1ff96947e79f74a9e33 b978bc78251698d86dd9a9eb6cb1d31b7be5dc01 ba9f3a0e514b318de12a41c858f61eb0405be6dd e828e640681af5a59eb109c490f5d83568b58f6d fa4602bf4fc1259dc08bdb65a78b49bdb66685aa" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -a -O--buildsystem=makefile cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=makefile dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb: building package 'subread' in '../subread_2.0.3+dfsg-1_amd64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.3+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../subread_2.0.3+dfsg-1_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/subread-CRk9SD /tmp/subread-2.0.3+dfsg-1skin24gy I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.BwYfkkVSsK... I: success in 397.4563 seconds md5: subread-dbgsym_2.0.3+dfsg-1_amd64.deb: OK md5: subread_2.0.3+dfsg-1_amd64.deb: OK sha1: subread-dbgsym_2.0.3+dfsg-1_amd64.deb: OK sha1: subread_2.0.3+dfsg-1_amd64.deb: OK sha256: subread-dbgsym_2.0.3+dfsg-1_amd64.deb: OK sha256: subread_2.0.3+dfsg-1_amd64.deb: OK Checksums: OK