Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/rna-star/rna-star_2.7.8a+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/rna-star-2.7.8a+dfsg-21h24iryn/rna-star_2.7.8a+dfsg-2_amd64.buildinfo Get source package info: rna-star=2.7.8a+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/rna-star/2.7.8a+dfsg-2/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 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 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+git20200708+dd9ef66-5 debconf=1.5.75 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 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=1.10-3 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=2.36.1-7 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.1-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.1 libcurl4-gnutls-dev=7.74.0-1.1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdpkg-perl=1.20.7.1 libelf1=0.183-1 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-7 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.7-2.1 libhts-dev=1.11-4 libhts3=1.11-4 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 libldap-2.4-2=2.4.57+dfsg-2 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma-dev=5.2.5-1.0 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.7-2.1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.2 libquadmath0=10.2.1-6 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsmartcols1=2.36.1-7 libssh2-1=1.9.0-2 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-1 libtasn1-6=4.16.0-2 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=247.3-1 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-2 linux-libc-dev=5.10.13-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 util-linux=2.36.1-7 vim-common=2:8.2.2434-2 xxd=2:8.2.2434-2 xz-utils=5.2.5-1.0 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/20210301T023626Z/ 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 rna-star=2.7.8a+dfsg-2 && mkdir -p /build/rna-star-vEzZTN && dpkg-source --no-check -x /*.dsc /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg && chown -R builduser:builduser /build/rna-star-vEzZTN" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1614626072" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/rna-star-vEzZTN /tmp/rna-star-2.7.8a+dfsg-21h24iryn bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210301T023626Z 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.dXoznjhPpJ 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.dXoznjhPpJ Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). 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/20210301T023626Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210301T023626Z 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 (1057 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 ... 4663 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 (2.31-9) ... 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/20210301T023626Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.dXoznjhPpJ Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210301T023626Z 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 19s (1186 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.dXoznjhPpJ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d rna-star=2.7.8a+dfsg-2 && mkdir -p /build/rna-star-vEzZTN && dpkg-source --no-check -x /*.dsc /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg && chown -R builduser:builduser /build/rna-star-vEzZTN"' exec /tmp/mmdebstrap.dXoznjhPpJ Reading package lists... NOTICE: 'rna-star' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rna-star.git Please use: git clone https://salsa.debian.org/med-team/rna-star.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 872 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rna-star 2.7.8a+dfsg-2 (dsc) [2196 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rna-star 2.7.8a+dfsg-2 (tar) [493 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rna-star 2.7.8a+dfsg-2 (diff) [377 kB] Fetched 872 kB in 1s (1293 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rna-star_2.7.8a+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting rna-star in /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg dpkg-source: info: unpacking rna-star_2.7.8a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.8a+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying simde.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1614626072" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.dXoznjhPpJ dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.8a+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_autoreconf_clean -O--sourcedirectory=source dh_clean -O--sourcedirectory=source debian/rules binary-arch dh binary-arch --sourcedirectory=source dh_update_autotools_config -a -O--sourcedirectory=source dh_autoreconf -a -O--sourcedirectory=source dh_auto_configure -a -O--sourcedirectory=source debian/rules override_dh_auto_build make[1]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' mkdir --parents /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -std=c++11 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_transformGenome.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:17: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | symlink("../../../SJ.out.tab", (outputPrefixMat+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:187:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 187 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:191:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 191 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bam_cat.c bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMoutput.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamRemoveDuplicates.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-avx2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx2 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' g++ -o STAR-avx -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' g++ -o STAR-sse4.1 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse4.1 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' g++ -o STAR-ssse3 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-ssse3 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' g++ -o STAR-sse3 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse3 -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain cd source && make -j10 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain make[2]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' g++ -o STAR-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=source dh_prep -a -O--sourcedirectory=source debian/rules override_dh_auto_install make[1]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' mkdir --parents /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/debian/rna-star/usr/bin dh_install source/STAR-avx2 source/STARlong-avx2 /usr/lib/rna-star/bin && dh_install source/STAR-avx source/STARlong-avx /usr/lib/rna-star/bin && dh_install source/STAR-sse4.1 source/STARlong-sse4.1 /usr/lib/rna-star/bin && dh_install source/STAR-ssse3 source/STARlong-ssse3 /usr/lib/rna-star/bin && dh_install source/STAR-sse3 source/STARlong-sse3 /usr/lib/rna-star/bin && dh_install source/STAR-plain source/STARlong-plain /usr/lib/rna-star/bin && true dh_install debian/bin/simd-dispatch /usr/lib/rna-star/ set -e && cd /build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg/debian/rna-star/usr/bin && for prog in STAR STARlong ; do ln -s \ ../lib/rna-star/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_installdocs -a -O--sourcedirectory=source dh_installchangelogs -a -O--sourcedirectory=source dh_installman -a -O--sourcedirectory=source dh_installsystemduser -a -O--sourcedirectory=source dh_perl -a -O--sourcedirectory=source dh_link -a -O--sourcedirectory=source dh_strip_nondeterminism -a -O--sourcedirectory=source debian/rules override_dh_compress make[1]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_fixperms -a -O--sourcedirectory=source dh_missing -a -O--sourcedirectory=source dh_dwz -a -a -O--sourcedirectory=source dh_strip -a -a -O--sourcedirectory=source dh_makeshlibs -a -a -O--sourcedirectory=source dh_shlibdeps -a -a -O--sourcedirectory=source dh_installdeb -a -O--sourcedirectory=source debian/rules override_dh_gencontrol make[1]: Entering directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/rna-star-vEzZTN/rna-star-2.7.8a+dfsg' dh_md5sums -a -O--sourcedirectory=source dh_builddeb -a -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.8a+dfsg-2_amd64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.8a+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rna-star_2.7.8a+dfsg-2_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/rna-star-vEzZTN /tmp/rna-star-2.7.8a+dfsg-21h24iryn I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.dXoznjhPpJ... I: success in 885.4441 seconds md5: rna-star-dbgsym_2.7.8a+dfsg-2_amd64.deb: OK md5: rna-star_2.7.8a+dfsg-2_amd64.deb: OK sha1: rna-star-dbgsym_2.7.8a+dfsg-2_amd64.deb: OK sha1: rna-star_2.7.8a+dfsg-2_amd64.deb: OK sha256: rna-star-dbgsym_2.7.8a+dfsg-2_amd64.deb: OK sha256: rna-star_2.7.8a+dfsg-2_amd64.deb: OK Checksums: OK