Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/rna-star/rna-star_2.7.9a+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/rna-star-2.7.9a+dfsg-3g43qt7n9/rna-star_2.7.9a+dfsg-3_amd64.buildinfo Get source package info: rna-star=2.7.9a+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/rna-star/2.7.9a+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.4-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-8 bsdutils=1:2.36.1-8 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.4+nmu1 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-8 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-13 libc-dev-bin=2.31-13 libc6=2.31-13 libc6-dev=2.31-13 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-2 libcrypt-dev=1:4.4.18-5 libcrypt1=1:4.4.18-5 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.4+nmu1 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdpkg-perl=1.20.9 libelf1=0.185-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-6 libhogweed6=3.7.3-1 libhts-dev=1.11-4 libhts3=1.11-4 libicu67=67.1-7 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 libldap-2.4-2=2.4.57+dfsg-3 liblsan0=10.2.1-6 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-8 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 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=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 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=2.36.1-8 libssh2-1=1.9.0-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-6 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=247.3-6 libunistring2=0.9.10-4 libuuid1=2.36.1-8 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 util-linux=2.36.1-8 vim-common=2:8.2.2434-3 xxd=2:8.2.2434-3 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210822T023545Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210822T023545Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210821T085836Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210815T204244Z/ 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=2.7.9a+dfsg-3 && mkdir -p /build/rna-star-eFxCLD && dpkg-source --no-check -x /*.dsc /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg && chown -R builduser:builduser /build/rna-star-eFxCLD" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629281625" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/rna-star-eFxCLD /tmp/rna-star-2.7.9a+dfsg-3g43qt7n9 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210815T204244Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.FIOb949WVB 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.FIOb949WVB Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-8). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210815T204244Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210815T204244Z 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 (1020 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4668 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-13) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210822T023545Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210822T023545Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210821T085836Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210815T204244Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.FIOb949WVB Get:1 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm InRelease [94.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210821T085836Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210815T204244Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main Sources [11.5 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210821T085836Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20210821T085836Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20210821T085836Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210821T085836Z unstable/main amd64 Packages [11.8 MB] Fetched 34.8 MB in 29s (1208 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.FIOb949WVB I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d rna-star=2.7.9a+dfsg-3 && mkdir -p /build/rna-star-eFxCLD && dpkg-source --no-check -x /*.dsc /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg && chown -R builduser:builduser /build/rna-star-eFxCLD"' exec /tmp/mmdebstrap.FIOb949WVB 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 990 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main rna-star 2.7.9a+dfsg-3 (dsc) [2225 B] Get:2 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main rna-star 2.7.9a+dfsg-3 (tar) [611 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210822T023545Z bookworm/main rna-star 2.7.9a+dfsg-3 (diff) [377 kB] Fetched 990 kB in 1s (1221 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rna-star_2.7.9a+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting rna-star in /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg dpkg-source: info: unpacking rna-star_2.7.9a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.9a+dfsg-3.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 do-not-enforce-avx2.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629281625" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.FIOb949WVB dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.9a+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' make[1]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg' mkdir --parents /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_clean ; dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_clean ; dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_clean ; dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_clean ; dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_clean ; dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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 -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.cpp 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); | ~~~~~~~~~~^~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-avx -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp In file included from opal.cpp:10: ./simde_avx2.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: ./simde_avx2.h:26437:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 26437 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-sse4.1 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp In file included from opal.cpp:10: ./simde_avx2.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: ./simde_avx2.h:26437:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 26437 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-ssse3 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp In file included from opal.cpp:10: ./simde_avx2.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: ./simde_avx2.h:26437:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 26437 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-sse3 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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-eFxCLD/rna-star-2.7.9a+dfsg/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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 -j4 clean make[2]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cd source && make -j4 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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_collapseUMIall_multiMappers.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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ClipMate_initialize.cpp In file included from opal.cpp:10: ./simde_avx2.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: ./simde_avx2.h:26437:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 26437 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_processRecords.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:20: 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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_samAttributes.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:189:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:193:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' ReadAlign_alignBAM.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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortByCoordinate.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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:253:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 253 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:254:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | 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-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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="2021-08-18T10:13:45+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Transcript.h:10:7: warning: type ‘struct Transcript’ violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ Transcript.h:10:7: note: a different type is defined in another translation unit 10 | class Transcript { | ^ Transcript.h:12:10: note: the first difference of corresponding definitions is field ‘exons’ 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:12:10: note: a field of same name but different type is defined in another translation unit 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:10:7: note: array types have different bounds 10 | class Transcript { | ^ ReadAlign.h:22:7: warning: type ‘struct ReadAlign’ violates the C++ One Definition Rule [-Wodr] 22 | class ReadAlign { | ^ ReadAlign.h:22:7: note: a different type is defined in another translation unit 22 | class ReadAlign { | ^ ReadAlign.h:57:20: note: the first difference of corresponding definitions is field ‘trA’ 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ ReadAlign.h:57:20: note: a field of same name but different type is defined in another translation unit 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ Transcript.h:10:7: note: type ‘struct Transcript’ itself violates the C++ One Definition Rule 10 | class Transcript { | ^ ReadAlign.h:210:14: warning: type of ‘calcCIGAR’ does not match original declaration [-Wlto-type-mismatch] 210 | void calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate); | ^ ReadAlign_calcCIGAR.cpp:3:6: note: ‘calcCIGAR’ was previously declared here 3 | void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) { | ^ In function ‘min’: lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function ‘min’: lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] opal/opal.cpp: In function ‘max’: opal/opal.cpp:763:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 763 | maxH = SIMD::max(maxH, H); // update best score in column | ^ In function ‘opalSearchDatabase’, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ opal/opal.cpp: In member function ‘mapChunk’: /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ opal/opal.cpp: In function ‘max’: opal/opal.cpp:763:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 763 | maxH = SIMD::max(maxH, H); // update best score in column | ^ In function ‘opalSearchDatabase’, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ opal/opal.cpp: In member function ‘mapChunk’: /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ opal/opal.cpp: In function ‘max’: opal/opal.cpp:752:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 752 | __mxxxi E = SIMD::max(SIMD::sub(prevHs[r], Q), SIMD::sub(prevEs[r], R)); // E could overflow | ^ opal/opal.cpp: In function ‘max’: opal/opal.cpp:752:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 752 | __mxxxi E = SIMD::max(SIMD::sub(prevHs[r], Q), SIMD::sub(prevEs[r], R)); // E could overflow | ^ make[2]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg' set -i; for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ debian/tests/run_test.sh /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-${SIMD} ; \ fi ; done /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-avx2 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:32 ..... started STAR run Nov 18 16:49:32 ... starting to generate Genome files Nov 18 16:49:32 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:32 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:32 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:32 ... loading chunks from disk, packing SA... Nov 18 16:49:32 ... finished generating suffix array Nov 18 16:49:32 ... generating Suffix Array index Nov 18 16:49:32 ... completed Suffix Array index Nov 18 16:49:32 ... writing Genome to disk ... Nov 18 16:49:32 ... writing Suffix Array to disk ... Nov 18 16:49:32 ... writing SAindex to disk Nov 18 16:49:32 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-avx2 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:32 ..... started STAR run Nov 18 16:49:32 ..... loading genome Nov 18 16:49:32 ..... started mapping Nov 18 16:49:33 ..... finished mapping Nov 18 16:49:33 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-avx --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:33 ..... started STAR run Nov 18 16:49:33 ... starting to generate Genome files Nov 18 16:49:33 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:33 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:33 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:33 ... loading chunks from disk, packing SA... Nov 18 16:49:33 ... finished generating suffix array Nov 18 16:49:33 ... generating Suffix Array index Nov 18 16:49:33 ... completed Suffix Array index Nov 18 16:49:33 ... writing Genome to disk ... Nov 18 16:49:33 ... writing Suffix Array to disk ... Nov 18 16:49:33 ... writing SAindex to disk Nov 18 16:49:33 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-avx --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:33 ..... started STAR run Nov 18 16:49:33 ..... loading genome Nov 18 16:49:33 ..... started mapping Nov 18 16:49:34 ..... finished mapping Nov 18 16:49:34 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-sse4.1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:34 ..... started STAR run Nov 18 16:49:34 ... starting to generate Genome files Nov 18 16:49:34 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:34 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:34 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:35 ... loading chunks from disk, packing SA... Nov 18 16:49:35 ... finished generating suffix array Nov 18 16:49:35 ... generating Suffix Array index Nov 18 16:49:35 ... completed Suffix Array index Nov 18 16:49:35 ... writing Genome to disk ... Nov 18 16:49:35 ... writing Suffix Array to disk ... Nov 18 16:49:35 ... writing SAindex to disk Nov 18 16:49:35 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-sse4.1 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:35 ..... started STAR run Nov 18 16:49:35 ..... loading genome Nov 18 16:49:35 ..... started mapping Nov 18 16:49:35 ..... finished mapping Nov 18 16:49:35 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-ssse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:35 ..... started STAR run Nov 18 16:49:35 ... starting to generate Genome files Nov 18 16:49:36 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:36 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:36 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:36 ... loading chunks from disk, packing SA... Nov 18 16:49:36 ... finished generating suffix array Nov 18 16:49:36 ... generating Suffix Array index Nov 18 16:49:36 ... completed Suffix Array index Nov 18 16:49:36 ... writing Genome to disk ... Nov 18 16:49:36 ... writing Suffix Array to disk ... Nov 18 16:49:36 ... writing SAindex to disk Nov 18 16:49:36 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-ssse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:36 ..... started STAR run Nov 18 16:49:36 ..... loading genome Nov 18 16:49:36 ..... started mapping Nov 18 16:49:36 ..... finished mapping Nov 18 16:49:37 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-sse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:37 ..... started STAR run Nov 18 16:49:37 ... starting to generate Genome files Nov 18 16:49:37 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:37 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:37 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:37 ... loading chunks from disk, packing SA... Nov 18 16:49:37 ... finished generating suffix array Nov 18 16:49:37 ... generating Suffix Array index Nov 18 16:49:37 ... completed Suffix Array index Nov 18 16:49:37 ... writing Genome to disk ... Nov 18 16:49:37 ... writing Suffix Array to disk ... Nov 18 16:49:37 ... writing SAindex to disk Nov 18 16:49:37 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/source/STAR-sse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:37 ..... started STAR run Nov 18 16:49:37 ..... loading genome Nov 18 16:49:37 ..... started mapping Nov 18 16:49:38 ..... finished mapping Nov 18 16:49:38 ..... finished successfully debian/tests/run_test.sh /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/tests/foo.gtf STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:38 ..... started STAR run Nov 18 16:49:38 ... starting to generate Genome files Nov 18 16:49:38 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Nov 18 16:49:38 ... starting to sort Suffix Array. This may take a long time... Nov 18 16:49:38 ... sorting Suffix Array chunks and saving them to disk... Nov 18 16:49:38 ... loading chunks from disk, packing SA... Nov 18 16:49:38 ... finished generating suffix array Nov 18 16:49:38 ... generating Suffix Array index Nov 18 16:49:38 ... completed Suffix Array index Nov 18 16:49:38 ... writing Genome to disk ... Nov 18 16:49:38 ... writing Suffix Array to disk ... Nov 18 16:49:38 ... writing SAindex to disk Nov 18 16:49:38 ..... finished successfully /build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.9a compiled: 2021-08-18T10:13:45+00:00 Nov 18 16:49:38 ..... started STAR run Nov 18 16:49:38 ..... loading genome Nov 18 16:49:38 ..... started mapping Nov 18 16:49:39 ..... finished mapping Nov 18 16:49:39 ..... finished successfully make[1]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg' mkdir --parents /build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+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-eFxCLD/rna-star-2.7.9a+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/rna-star-eFxCLD/rna-star-2.7.9a+dfsg' dh_md5sums -a -O--sourcedirectory=source dh_builddeb -a -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.9a+dfsg-3_amd64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.9a+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rna-star_2.7.9a+dfsg-3_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-eFxCLD /tmp/rna-star-2.7.9a+dfsg-3g43qt7n9 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.FIOb949WVB... I: success in 2657.8128 seconds md5: rna-star-dbgsym_2.7.9a+dfsg-3_amd64.deb: OK md5: rna-star_2.7.9a+dfsg-3_amd64.deb: OK sha1: rna-star-dbgsym_2.7.9a+dfsg-3_amd64.deb: OK sha1: rna-star_2.7.9a+dfsg-3_amd64.deb: OK sha256: rna-star-dbgsym_2.7.9a+dfsg-3_amd64.deb: OK sha256: rna-star_2.7.9a+dfsg-3_amd64.deb: OK Checksums: OK