Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/subread/subread_2.0.1+dfsg-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/subread-2.0.1+dfsg-12o9ill6l/subread_2.0.1+dfsg-1_all.buildinfo Get source package info: subread=2.0.1+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/subread/2.0.1+dfsg-1/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 bc=1.07.1-2+b2 binutils=2.34-8 binutils-common=2.34-8 binutils-x86-64-linux-gnu=2.34-8 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=9.3.0-13 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.1 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=1:5.38-5 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-13 gcc=4:9.2.1-3.1 gcc-10-base=10.1.0-2 gcc-9=9.3.0-13 gcc-9-base=9.3.0-13 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 help2man=1.47.15 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=9.3.0-13 libatomic1=10.1.0-2 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34-8 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=10.1.0-2 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34-8 libctf0=2.34-8 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.252 libdebhelper-perl=13.1 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libgcc-9-dev=9.3.0-13 libgcc-s1=10.1.0-2 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=10.1.0-2 libgpg-error0=1.37-1 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10.1.0-2 liblocale-gettext-perl=1.07-4 liblsan0=10.1.0-2 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.35.1-5 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.0.2-1 libncurses6=6.2-1 libncursesw6=6.2-1 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=5.30.2-1 libpipeline1=1.5.2-2 libpython3-stdlib=3.8.2-3 libpython3.8-minimal=3.8.3-1 libpython3.8-stdlib=3.8.3-1 libquadmath0=10.1.0-2 libreadline8=8.0-4 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.35.1-5 libsqlite3-0=3.31.1-5 libssl1.1=1.1.1g-1 libstdc++-9-dev=9.3.0-13 libstdc++6=10.1.0-2 libsub-override-perl=0.09-2 libsystemd0=245.5-3 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.1.0-2 libubsan1=10.1.0-2 libuchardet0=0.0.6-3 libudev1=245.5-3 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 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.2-1 perl-base=5.30.2-1 perl-modules-5.30=5.30.2-1 po-debconf=1.0.21 python3=3.8.2-3 python3-minimal=3.8.2-3 python3.8=3.8.3-1 python3.8-minimal=3.8.3-1 readline-common=8.0-4 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 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200520T205149Z/ 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=2.0.1+dfsg-1 && mkdir -p /build/subread-eMR2Aa && dpkg-source --no-check -x /*.dsc /build/subread-eMR2Aa/subread-2.0.1+dfsg && chown -R builduser:builduser /build/subread-eMR2Aa" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/subread-eMR2Aa/subread-2.0.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1590168680" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/subread-eMR2Aa /tmp/subread-2.0.1+dfsg-12o9ill6l bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200520T205149Z 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.Ir5JRVDX0D 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.Ir5JRVDX0D 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/20200520T205149Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200520T205149Z 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 (1054 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/20200520T205149Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Ir5JRVDX0D Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200520T205149Z 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 21s (1050 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.Ir5JRVDX0D I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d subread=2.0.1+dfsg-1 && mkdir -p /build/subread-eMR2Aa && dpkg-source --no-check -x /*.dsc /build/subread-eMR2Aa/subread-2.0.1+dfsg && chown -R builduser:builduser /build/subread-eMR2Aa"' exec /tmp/mmdebstrap.Ir5JRVDX0D 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 13.7 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main subread 2.0.1+dfsg-1 (dsc) [2303 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main subread 2.0.1+dfsg-1 (tar) [13.7 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main subread 2.0.1+dfsg-1 (diff) [10.3 kB] Fetched 13.7 MB in 11s (1198 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'subread_2.0.1+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting subread in /build/subread-eMR2Aa/subread-2.0.1+dfsg dpkg-source: info: unpacking subread_2.0.1+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_2.0.1+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 gcc10.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/subread-eMR2Aa/subread-2.0.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1590168680" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.Ir5JRVDX0D dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+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 make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+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-eMR2Aa/subread-2.0.1+dfsg/src' dh_clean 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg/src' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c input-files.c: In function ‘is_SAM_unsorted’: input-files.c:6237:33: warning: ‘read_name[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6237 | for(field_cursor = 0; read_name[field_cursor] ; field_cursor++) | ~~~~~~~~~^~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 cd longread-one && make make[3]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg/src/longread-one' gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMbase-index.o -c LRMbase-index.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMchro-event.o -c LRMchro-event.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhelper.o -c LRMhelper.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMseek-zlib.o -c LRMseek-zlib.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMfile-io.o -c LRMfile-io.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhashtable.o -c LRMhashtable.c gcc -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -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 make[3]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg/src/longread-one' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 readSummary.c: In function ‘fc_thread_start_threads’: readSummary.c:5194:28: warning: ‘%s’ directive writing up to 1019 bytes into a region of size between 100 and 1099 [-Wformat-overflow=] 5194 | sprintf(tmp_fname2, "%s/%s", applied_detail_path, modified_fname); | ^~ In file included from /usr/include/stdio.h:867, from readSummary.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 2020 bytes into a destination of size 1100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 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: 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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-eMR2Aa/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 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-eMR2Aa/subread-2.0.1+dfsg/src' dh_auto_build -- CC=x86_64-linux-gnu-gcc make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' rm -f debian/subread-data.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' debian/tests/subread-tests /build/subread-eMR2Aa/subread-2.0.1+dfsg  ************************************************** ************************************************** *** *** *** This script will test the major functions *** *** in our package, including the index build- *** *** er, subread-align, subjunc, featureCounts *** *** and exactSNP. *** *** *** *** Test will start in seconds. *** *** *** ************************************************** ************************************************** 9876543210[0,0H ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 87.6GB / 125.9GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=1197.6k bps/s || || 16%, 0 mins elapsed, rate=1972.5k bps/s || || 25%, 0 mins elapsed, rate=2515.0k bps/s || || 33%, 0 mins elapsed, rate=2915.9k bps/s || || 41%, 0 mins elapsed, rate=3326.7k bps/s || || 50%, 0 mins elapsed, rate=3618.6k bps/s || || 58%, 0 mins elapsed, rate=3392.0k bps/s || || 66%, 0 mins elapsed, rate=3586.4k bps/s || || 75%, 0 mins elapsed, rate=3735.1k bps/s || || 83%, 0 mins elapsed, rate=3881.1k bps/s || || 91%, 0 mins elapsed, rate=3992.0k bps/s || || 100%, 0 mins elapsed, rate=3712.1k bps/s || || 1.3 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=75.9k bps/s || || 16%, 0 mins elapsed, rate=142.7k bps/s || || 25%, 0 mins elapsed, rate=206.3k bps/s || || 33%, 0 mins elapsed, rate=262.2k bps/s || || 41%, 0 mins elapsed, rate=317.8k bps/s || || 50%, 0 mins elapsed, rate=365.5k bps/s || || 58%, 0 mins elapsed, rate=415.0k bps/s || || 66%, 0 mins elapsed, rate=455.3k bps/s || || 75%, 0 mins elapsed, rate=499.3k bps/s || || 83%, 0 mins elapsed, rate=538.4k bps/s || || 91%, 0 mins elapsed, rate=577.1k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.1 minutes. || || Index ../small1 was successfully built! || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:38:15, pid=1779908) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.7 mins elapsed, rate=20.0k reads per second || || 74% completed, 0.7 mins elapsed, rate=0.4k reads per second || || 83% completed, 0.7 mins elapsed, rate=0.4k reads per second || || 91% completed, 0.7 mins elapsed, rate=0.4k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 0.7 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:38:57, pid=1779912) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.7 mins elapsed, rate=36.0k reads per second || || 74% completed, 0.7 mins elapsed, rate=0.4k reads per second || || 83% completed, 0.7 mins elapsed, rate=0.4k reads per second || || 91% completed, 0.7 mins elapsed, rate=0.4k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 0.7 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:39:39, pid=1779916) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.8 mins elapsed, rate=4.4k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 0.8 mins elapsed, rate=0.3k fragments per second || || 83% completed, 0.8 mins elapsed, rate=0.3k fragments per second || || 91% completed, 0.8 mins elapsed, rate=0.4k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 0.8 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:40:29, pid=1779920) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.6 mins elapsed, rate=14.9k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 0.6 mins elapsed, rate=0.4k fragments per second || || 83% completed, 0.6 mins elapsed, rate=0.4k fragments per second || || 91% completed, 0.7 mins elapsed, rate=0.5k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 0.7 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-error-r1.fq || || Input file 2 : test-error-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:41:09, pid=1779924) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [-14,-14] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.7 mins elapsed, rate=11.3k fragments per second || || Estimated fragment length : 497 bp || || 74% completed, 0.7 mins elapsed, rate=0.4k fragments per second || || 83% completed, 0.7 mins elapsed, rate=0.4k fragments per second || || 91% completed, 0.7 mins elapsed, rate=0.4k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 20000 || || Mapped : 18937 (94.7%) || || Uniquely mapped : 18937 || || Multi-mapping : 0 || || || || Unmapped : 1063 || || || || Properly paired : 14143 || || Not properly paired : 4794 || || Singleton : 4504 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 274 || || Unexpected read order : 16 || || || || Indels : 15 || || || || Running time : 0.7 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-err-mut-r1.fq.gz || || Input file 2 : test-err-mut-r2.fq.gz || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || Read group name : MyTestGroup || || || \\============================================================================// //=============== Running (11-Oct-2021 06:41:54, pid=1779928) ================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 174b4933011d38e29cacd5c81cd2bebd ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** SINGLE-END READS NO ERROR NO DUP ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** READS WITH NO ERROR ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS NO ERROR, NO DUPLICATED REPORT ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS WITH ONLY SEQUENCING ERROR ****** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Memory : 8000 Mbytes || || Repeat threshold : 100 repeats || || Gapped index : yes || || || || Free / total memory : 90.1GB / 125.9GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=7621.1k bps/s || || 16%, 0 mins elapsed, rate=9314.7k bps/s || || 25%, 0 mins elapsed, rate=9672.9k bps/s || || 33%, 0 mins elapsed, rate=10161.5k bps/s || || 41%, 0 mins elapsed, rate=10747.7k bps/s || || 50%, 0 mins elapsed, rate=10934.6k bps/s || || 58%, 0 mins elapsed, rate=7824.3k bps/s || || 66%, 0 mins elapsed, rate=7451.7k bps/s || || 75%, 0 mins elapsed, rate=7544.9k bps/s || || 83%, 0 mins elapsed, rate=7762.2k bps/s || || 91%, 0 mins elapsed, rate=8018.7k bps/s || || 100%, 0 mins elapsed, rate=8245.8k bps/s || || 0.6 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=558.9k bps/s || || 16%, 0 mins elapsed, rate=1035.0k bps/s || || 25%, 0 mins elapsed, rate=1437.1k bps/s || || 33%, 0 mins elapsed, rate=1619.9k bps/s || || 41%, 0 mins elapsed, rate=1888.1k bps/s || || 50%, 0 mins elapsed, rate=2158.8k bps/s || || 58%, 0 mins elapsed, rate=2405.0k bps/s || || 66%, 0 mins elapsed, rate=2640.4k bps/s || || 75%, 0 mins elapsed, rate=2836.4k bps/s || || 83%, 0 mins elapsed, rate=2748.6k bps/s || || 91%, 0 mins elapsed, rate=2881.7k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.1 minutes. || || Index ../small1 was successfully built! || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctions.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 14 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:41:58, pid=1779935) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=9.5k fragments per second || || Estimated fragment length : 173 bp || || 77% completed, 0.1 mins elapsed, rate=1.9k fragments per second || || 87% completed, 0.1 mins elapsed, rate=2.0k fragments per second || || 97% completed, 0.1 mins elapsed, rate=2.2k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15291 (95.3%) || || Uniquely mapped : 15291 || || Multi-mapping : 0 || || || || Unmapped : 761 || || || || Properly paired : 13894 || || Not properly paired : 1397 || || Singleton : 962 || || Chimeric : 0 || || Unexpected strandness : 36 || || Unexpected fragment length : 335 || || Unexpected read order : 64 || || || || Junctions : 419 || || Indels : 177 || || || || Running time : 0.1 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctionsNfusions.bam (BAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 28 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (11-Oct-2021 06:42:06, pid=1779937) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output BAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=4.7k fragments per second || || Estimated fragment length : 174 bp || || 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || || 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second || || 97% completed, 0.2 mins elapsed, rate=1.6k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15273 (95.1%) || || Uniquely mapped : 15273 || || Multi-mapping : 0 || || || || Unmapped : 779 || || || || Properly paired : 13793 || || Not properly paired : 1480 || || Singleton : 1013 || || Chimeric : 0 || || Unexpected strandness : 37 || || Unexpected fragment length : 368 || || Unexpected read order : 62 || || || || Junctions : 437 || || Fusions : 33 || || Indels : 180 || || || || Running time : 0.2 minutes || || || \\============================================================================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || o test-minimum.sam || || || || Output file : test-minimum.FC || || Summary : test-minimum.FC.summary || || Annotation : test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file test-minimum.sam... || || WARNING: Paired-end reads were found. || || Total alignments : 998 || || Successfully assigned alignments : 389 (39.0%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "result/test-minimum.FC. || || summary" || || || \\============================================================================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //============================= exactSNP setting =============================\\ || || || Input file : test-in.BAM (BAM) || || Output file : test-out.VCF || || Reference genome : chr901.fa || || Temp path : || || || || Threads : 1 || || Min supporting reads : 1 || || Min pct. of supporting reads : 0.0% || || Min base quality score : 13 || || Number of trimmed bases : 3 || || || || Q value cutoff : 10E-12.0 || || P value upper bound : 0.00500 || || Flanking windows size : 5 || || || \\============================================================================// //====================== Running (11-Oct-2021 06:42:18) ======================\\ || || || Split BAM file into result/temp-snps-1780476-0242AC15001F-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed reads : 50204 || || Reported SNPs : 416 || || Reported indels : 22 || || || || Running time : 0.0 minutes || || || \\============================================================================//  ************************************************** ************************************************** *** *** *** Test finished. *** *** *** *** Should there be any error, please visit *** *** http://subread.sourceforge.net/ for more *** *** information. *** *** *** ************************************************** **************************************************  make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i rm -f -- debian/subread-data.substvars rm -fr -- debian/.debhelper/generated/subread-data/ debian/subread-data/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' find /build/subread-eMR2Aa/subread-2.0.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1 help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/subread-align | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1; help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/subread-buildindex | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1; help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/subjunc | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/featureCounts | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/exactSNP | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/subindel | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subindel.1; help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/sublong| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/sublong.1; help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1; help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1; help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/qualityScores| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/qualityScores.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \ to each other in the output. A dummy read is added for each singleton read that does not have a pair. \ The output file is compatible with featureCounts program' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/repair| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/repair.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/removeDup| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/removeDup.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \ to a SAF format file.' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1; help2man --no-info --help-option="''" --no-discard-stderr --name='helper tool from subread suite' \ /build/subread-eMR2Aa/subread-2.0.1+dfsg/bin/utilities/genRandomReads| debian/filter.pl > /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/genRandomReads.1; dh_auto_install install -d /build/subread-eMR2Aa/subread-2.0.1\+dfsg/debian/tmp make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' dh_install -i install -d debian/.debhelper/generated/subread install -d debian/subread-data/usr/share/doc/subread/examples cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/ install -d debian/.debhelper/generated/subread-data dh_installdocs -i install -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -i install -p -m0644 debian/changelog debian/subread-data/usr/share/doc/subread-data/changelog.Debian rm -f debian/subread-data.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' tar --sort=name \ --mtime="@1590168680" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ -cJf /build/subread-eMR2Aa/subread-2.0.1+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ make[1]: Leaving directory '/build/subread-eMR2Aa/subread-2.0.1+dfsg' dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i cd debian/subread-data chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt cd '/build/subread-eMR2Aa/subread-2.0.1+dfsg' dh_fixperms -i find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread-data -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 dh_missing -i dh_installdeb -i install -d debian/subread-data/DEBIAN dh_gencontrol -i echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -Pdebian/subread-data dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined chmod 0644 -- debian/subread-data/DEBIAN/control dh_md5sums -i cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums dh_builddeb -i dpkg-deb --root-owner-group --build debian/subread-data .. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../subread_2.0.1+dfsg-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/subread-eMR2Aa /tmp/subread-2.0.1+dfsg-12o9ill6l I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.Ir5JRVDX0D... I: success in 818.5049 seconds md5: subread-data_2.0.1+dfsg-1_all.deb: OK sha1: subread-data_2.0.1+dfsg-1_all.deb: OK sha256: subread-data_2.0.1+dfsg-1_all.deb: OK Checksums: OK