I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 7 09:58:18 +14 2021 I: pbuilder-time-stamp: 1625601498 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rna-star_2.7.8a+dfsg-2.dsc] I: copying [./rna-star_2.7.8a+dfsg.orig.tar.xz] I: copying [./rna-star_2.7.8a+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.zndA6OGG/trustedkeys.kbx': General error gpgv: Signature made Tue Mar 2 09:15:58 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.8a+dfsg-2.dsc dpkg-source: info: extracting rna-star in rna-star-2.7.8a+dfsg dpkg-source: info: unpacking rna-star_2.7.8a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.8a+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying simde.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22524/tmp/hooks/D01_modify_environment starting debug: Running on codethink10-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/22524/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/22524/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=22524 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.RVvVvB8LII/pbuilderrc_FFZZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RVvVvB8LII/b2 --logfile b2/build.log --extrapackages usrmerge rna-star_2.7.8a+dfsg-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 7 09:58 sh -> bash lrwxrwxrwx 1 root root 4 Jul 5 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/22524/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on vim-common; however: Package vim-common is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} vim-common{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix vim vim-athena vim-gtk3 vim-nox vim-tiny wget 0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 25.1 MB of archives. After unpacking 84.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 xxd arm64 2:8.2.2434-3 [192 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 vim-common all 2:8.2.2434-3 [226 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3 [317 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3 [419 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libsimde-dev all 0.7.2-4 [259 kB] Fetched 25.1 MB in 0s (55.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package xxd. Preparing to unpack .../06-xxd_2%3a8.2.2434-3_arm64.deb ... Unpacking xxd (2:8.2.2434-3) ... Selecting previously unselected package vim-common. Preparing to unpack .../07-vim-common_2%3a8.2.2434-3_all.deb ... Unpacking vim-common (2:8.2.2434-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../09-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../12-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. 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Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:arm64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (2671 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 22081 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... 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I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/rna-star-2.7.8a+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rna-star_2.7.8a+dfsg-2_source.changes dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.8a+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/rna-star-2.7.8a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/build/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' dh_autoreconf_clean -O--sourcedirectory=source dh_clean -O--sourcedirectory=source debian/rules binary dh binary --sourcedirectory=source dh_update_autotools_config -O--sourcedirectory=source dh_autoreconf -O--sourcedirectory=source dh_auto_configure -O--sourcedirectory=source debian/rules override_dh_auto_build make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' dh_auto_build -- CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR STARlong cd source && make -j8 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR STARlong make[2]: Entering directory '/build/rna-star-2.7.8a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_convertGenomeCigar.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:41:17: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | symlink("../../../SJ.out.tab", (outputPrefixMat+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:187:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 187 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:191:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' serviceFuns.cpp 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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' 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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortUnmapped.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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~ 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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -fdebug-prefix-map=/build/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) { | ^ make[2]: Leaving directory '/build/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' debian/tests/run_test.sh /build/rna-star-2.7.8a+dfsg/source/STAR Jul 07 10:05:14 ..... started STAR run Jul 07 10:05:14 ... starting to generate Genome files Jul 07 10:05:14 ..... 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 Jul 07 10:05:14 ... starting to sort Suffix Array. This may take a long time... Jul 07 10:05:14 ... sorting Suffix Array chunks and saving them to disk... Jul 07 10:05:14 ... loading chunks from disk, packing SA... Jul 07 10:05:14 ... finished generating suffix array Jul 07 10:05:14 ... generating Suffix Array index Jul 07 10:05:14 ... completed Suffix Array index Jul 07 10:05:14 ... writing Genome to disk ... Jul 07 10:05:14 ... writing Suffix Array to disk ... Jul 07 10:05:14 ... writing SAindex to disk Jul 07 10:05:14 ..... finished successfully Jul 07 10:05:14 ..... started STAR run Jul 07 10:05:14 ..... loading genome Jul 07 10:05:14 ..... started mapping Jul 07 10:05:15 ..... finished mapping Jul 07 10:05:15 ..... finished successfully make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=source dh_prep -O--sourcedirectory=source debian/rules override_dh_auto_install make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' dh_install source/STAR source/STARlong usr/bin/ make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' dh_installdocs -O--sourcedirectory=source dh_installchangelogs -O--sourcedirectory=source dh_installman -O--sourcedirectory=source dh_installsystemduser -O--sourcedirectory=source dh_perl -O--sourcedirectory=source dh_link -O--sourcedirectory=source dh_strip_nondeterminism -O--sourcedirectory=source debian/rules override_dh_compress make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' dh_fixperms -O--sourcedirectory=source dh_missing -O--sourcedirectory=source dh_dwz -a -O--sourcedirectory=source dh_strip -a -O--sourcedirectory=source dh_makeshlibs -a -O--sourcedirectory=source dh_shlibdeps -a -O--sourcedirectory=source dh_installdeb -O--sourcedirectory=source debian/rules override_dh_gencontrol make[1]: Entering directory '/build/rna-star-2.7.8a+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/rna-star-2.7.8a+dfsg' dh_md5sums -O--sourcedirectory=source dh_builddeb -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.8a+dfsg-2_arm64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.8a+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rna-star_2.7.8a+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/22524/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/22524/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/22524 and its subdirectories I: Current time: Wed Jul 7 10:06:32 +14 2021 I: pbuilder-time-stamp: 1625601992