Thu Jan 11 15:56:56 UTC 2024 I: starting to build rna-star/bookworm/amd64 on jenkins on '2024-01-11 15:56' Thu Jan 11 15:56:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/9618/console.log Thu Jan 11 15:56:56 UTC 2024 I: Downloading source for bookworm/rna-star=2.7.10b+dfsg-2 --2024-01-11 15:56:56-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/rna-star/rna-star_2.7.10b%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2158 (2.1K) [text/prs.lines.tag] Saving to: ‘rna-star_2.7.10b+dfsg-2.dsc’ 0K .. 100% 282M=0s 2024-01-11 15:56:56 (282 MB/s) - ‘rna-star_2.7.10b+dfsg-2.dsc’ saved [2158/2158] Thu Jan 11 15:56:56 UTC 2024 I: rna-star_2.7.10b+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 ppc64el mips64el Version: 2.7.10b+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss , Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libhts-dev, xxd, zlib1g-dev, libsimde-dev Package-List: rna-star deb science optional arch=amd64,arm64,ppc64el,mips64el Checksums-Sha1: 38cedf2bdb3420d87f32466578913d4312d50d41 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 253f000719fb12c4e037d3066c85d024c32ac2b6 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz Checksums-Sha256: 77b61638b3eda7f429364b1f1ff8fc806d95ee55a3c5992c25b29a641c9a83c4 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 62fb8dac5feb22cbcab53c12e57dac4a4f6763171f67d0c8c3b3ee12ff1645d3 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz Files: 20e0f5ac4f2da8d32502a153fbdd2815 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 806af201cdfd2517402e3db64006d400 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmPNSjAACgkQPCZ2P2xn 5uLkKBAAmzwtNuFiuRbG2ACCTOdOI0ELa9HAZ7lsIzg+1stnlzXHpja1Y9Qm34kA OaG8dKXq4fecVkPXnD+1ff4cxx9w0c+HbfRcBVPAVfGBo2Y1xscttQARoq/3WNcf Lxfr41n7HOXjNySNAWcY+SLlYbGPsg9W5oMAPsHY90avp7Z9t+JgMn6rqsaWqxpf 7PJ5lWS4G460yZVV+B1U0vc2oeFQS42TTgsHESa5WHeihSi9UWV7M3thfCtmDjgy 1VvNKmV8tLrhQQFdf7v32GiTK9csI6fzNnBMzvUo9TiE5+QnzGpAyUQpjR+d9XIb UJGcBHtL+cNALxWqqyAkut32EpE4hrJV33VHh0W/YIXvwi/u32Lz/YfVa+YDEcIh Lfi32D5PnE7lGJdZwEixrSM8ChpYlkU41LlzDzEDLoWa8hO8L+o57jaB8VK8FghK M9/oEWzC1QrbEvYjCO8xGWLybb9on6nYcQq7VJJXoUU2xSkliBXi+wmj6YKwkVPp g3zhROq5NZrT7ISdGkUfq/29NdJ7aSalCHg6KNA7UeBupX3cub4uNRTP33Rzi5kh jdhfFmefStg3Zd60dS6Ktd5CNkc0Kz+37h84uN6jgdkjd+ez2iVZ9xCeKzO2f/Ik AU69pHcgLJHX0SW1K/j0waA/iebraMc7dLCU2kssYXcVi3OJLxI= =j9Xr -----END PGP SIGNATURE----- Thu Jan 11 15:56:56 UTC 2024 I: Checking whether the package is not for us Thu Jan 11 15:56:56 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Jan 11 15:56:56 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Jan 11 16:16:46 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 11 03:56:59 -12 2024 I: pbuilder-time-stamp: 1704988619 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_2.7.10b+dfsg-2.dsc] I: copying [./rna-star_2.7.10b+dfsg.orig.tar.xz] I: copying [./rna-star_2.7.10b+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 22 14:37:36 2023 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.10b+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting rna-star in rna-star-2.7.10b+dfsg dpkg-source: info: unpacking rna-star_2.7.10b+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.10b+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 do-not-enforce-avx2.patch dpkg-source: info: applying gcc-12.patch dpkg-source: info: applying packaged_simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2569962/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1cb79a0c1acc43829acb5f3ca0b1b9f2' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2569962' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/pbuilderrc_B5CN --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/b1 --logfile b1/build.log rna-star_2.7.10b+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2569962/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: amd64 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, 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 ... 18148 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 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} libhtscodecs2{a} libicu72{a} libldap-2.5-0{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} 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} 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 wget 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After unpacking 94.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10+deb12u4 [485 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 xxd amd64 2:9.0.1378-2 [83.7 kB] Fetched 24.4 MB in 1s (17.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 18148 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../30-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../31-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../32-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../33-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../34-libnghttp2-14_1.52.0-1+deb12u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../35-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../36-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../37-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../38-libcurl3-gnutls_7.88.1-10+deb12u4_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-10+deb12u4) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../39-libcurl4-gnutls-dev_7.88.1-10+deb12u4_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.88.1-10+deb12u4) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../40-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../41-libdeflate-dev_1.14-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../42-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../43-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../44-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../45-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../46-libhts-dev_1.16+ds-3_amd64.deb ... Unpacking libhts-dev:amd64 (1.16+ds-3) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../47-libsimde-dev_0.7.4~rc2-2_all.deb ... Unpacking libsimde-dev (0.7.4~rc2-2) ... Selecting previously unselected package xxd. Preparing to unpack .../48-xxd_2%3a9.0.1378-2_amd64.deb ... Unpacking xxd (2:9.0.1378-2) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libsimde-dev (0.7.4~rc2-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up xxd (2:9.0.1378-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u4) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-10+deb12u4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... 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 I: Building the package I: Running cd /build/reproducible-path/rna-star-2.7.10b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rna-star_2.7.10b+dfsg-2_source.changes dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.10b+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+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/reproducible-path/rna-star-2.7.10b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_clean ; dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_clean ; dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_clean ; dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_clean ; dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_clean ; dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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); | ~~~~~~~~~~^~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | 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-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | 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-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | 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-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | 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-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain cd source && make -j15 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+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_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.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 systemFunctions.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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.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()); | ~~~~~~^~~~~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::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); | ~~~~~~~~~~^~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.o 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 Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp 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 Transcript.h:10:7: warning: type 'struct Transcript' violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ Transcript.h:10:7: note: a different type is defined in another translation unit 10 | class Transcript { | ^ Transcript.h:12:10: note: the first difference of corresponding definitions is field 'exons' 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:12:10: note: a field of same name but different type is defined in another translation unit 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:10:7: note: array types have different bounds 10 | class Transcript { | ^ ReadAlign.h:22:7: warning: type 'struct ReadAlign' violates the C++ One Definition Rule [-Wodr] 22 | class ReadAlign { | ^ ReadAlign.h:22:7: note: a different type is defined in another translation unit 22 | class ReadAlign { | ^ ReadAlign.h:57:20: note: the first difference of corresponding definitions is field 'trA' 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ ReadAlign.h:57:20: note: a field of same name but different type is defined in another translation unit 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ Transcript.h:10:7: note: type 'struct Transcript' itself violates the C++ One Definition Rule 10 | class Transcript { | ^ ReadAlign.h:210:14: warning: type of 'calcCIGAR' does not match original declaration [-Wlto-type-mismatch] 210 | void calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate); | ^ ReadAlign_calcCIGAR.cpp:3:6: note: 'calcCIGAR' was previously declared here 3 | void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) { | ^ In function 'min': lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function 'min': lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] lto-wrapper: warning: using serial compilation of 24 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information lto-wrapper: warning: using serial compilation of 24 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information In function 'searchDatabase_', inlined from 'searchDatabase' at opal/opal.cpp:1013:21, inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/include/c++/12/new: In member function 'mapChunk': /usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'searchDatabase_', inlined from 'searchDatabase' at opal/opal.cpp:1013:21, inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/include/c++/12/new: In member function 'mapChunk': /usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'assign', inlined from '_M_set_length' at /usr/include/c++/12/bits/basic_string.h:268:21, inlined from '__ct ' at /usr/include/c++/12/bits/basic_string.h:520:15, inlined from 'signalFromBAM' at signalFromBAM.cpp:44:43: /usr/include/c++/12/bits/char_traits.h:354:14: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 354 | __c1 = __c2; | ^ signalFromBAM.cpp: In function 'signalFromBAM': signalFromBAM.cpp:44:43: note: at offset 152 into destination object of size [72, 136] allocated by 'operator new []' 44 | string* sigOutFileName=new string[sigN]; | ^ In function 'assign', inlined from '_M_set_length' at /usr/include/c++/12/bits/basic_string.h:268:21, inlined from '__ct ' at /usr/include/c++/12/bits/basic_string.h:520:15, inlined from 'signalFromBAM' at signalFromBAM.cpp:44:43: /usr/include/c++/12/bits/char_traits.h:354:14: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 354 | __c1 = __c2; | ^ signalFromBAM.cpp: In function 'signalFromBAM': signalFromBAM.cpp:44:43: note: at offset 152 into destination object of size [72, 136] allocated by 'operator new []' 44 | string* sigOutFileName=new string[sigN]; | ^ opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' set -i; for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-${SIMD} ; \ fi ; done /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-avx --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:40 ..... started STAR run Jan 11 16:13:40 ... starting to generate Genome files Jan 11 16:13:40 ..... 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 Jan 11 16:13:40 ... starting to sort Suffix Array. This may take a long time... Jan 11 16:13:40 ... sorting Suffix Array chunks and saving them to disk... Jan 11 16:13:40 ... loading chunks from disk, packing SA... Jan 11 16:13:40 ... finished generating suffix array Jan 11 16:13:40 ... generating Suffix Array index Jan 11 16:13:40 ... completed Suffix Array index Jan 11 16:13:40 ... writing Genome to disk ... Jan 11 16:13:40 ... writing Suffix Array to disk ... Jan 11 16:13:40 ... writing SAindex to disk Jan 11 16:13:40 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-avx --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:40 ..... started STAR run Jan 11 16:13:40 ..... loading genome Jan 11 16:13:40 ..... started mapping Jan 11 16:13:41 ..... finished mapping Jan 11 16:13:41 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse4.1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:41 ..... started STAR run Jan 11 16:13:41 ... starting to generate Genome files Jan 11 16:13:41 ..... 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 Jan 11 16:13:41 ... starting to sort Suffix Array. This may take a long time... Jan 11 16:13:41 ... sorting Suffix Array chunks and saving them to disk... Jan 11 16:13:41 ... loading chunks from disk, packing SA... Jan 11 16:13:41 ... finished generating suffix array Jan 11 16:13:41 ... generating Suffix Array index Jan 11 16:13:41 ... completed Suffix Array index Jan 11 16:13:41 ... writing Genome to disk ... Jan 11 16:13:41 ... writing Suffix Array to disk ... Jan 11 16:13:41 ... writing SAindex to disk Jan 11 16:13:41 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse4.1 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:41 ..... started STAR run Jan 11 16:13:41 ..... loading genome Jan 11 16:13:41 ..... started mapping Jan 11 16:13:42 ..... finished mapping Jan 11 16:13:42 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-ssse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:42 ..... started STAR run Jan 11 16:13:42 ... starting to generate Genome files Jan 11 16:13:42 ..... 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 Jan 11 16:13:42 ... starting to sort Suffix Array. This may take a long time... Jan 11 16:13:42 ... sorting Suffix Array chunks and saving them to disk... Jan 11 16:13:42 ... loading chunks from disk, packing SA... Jan 11 16:13:42 ... finished generating suffix array Jan 11 16:13:42 ... generating Suffix Array index Jan 11 16:13:42 ... completed Suffix Array index Jan 11 16:13:42 ... writing Genome to disk ... Jan 11 16:13:42 ... writing Suffix Array to disk ... Jan 11 16:13:42 ... writing SAindex to disk Jan 11 16:13:42 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-ssse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:42 ..... started STAR run Jan 11 16:13:42 ..... loading genome Jan 11 16:13:42 ..... started mapping Jan 11 16:13:43 ..... finished mapping Jan 11 16:13:43 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:43 ..... started STAR run Jan 11 16:13:43 ... starting to generate Genome files Jan 11 16:13:43 ..... 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 Jan 11 16:13:43 ... starting to sort Suffix Array. This may take a long time... Jan 11 16:13:43 ... sorting Suffix Array chunks and saving them to disk... Jan 11 16:13:43 ... loading chunks from disk, packing SA... Jan 11 16:13:43 ... finished generating suffix array Jan 11 16:13:43 ... generating Suffix Array index Jan 11 16:13:43 ... completed Suffix Array index Jan 11 16:13:43 ... writing Genome to disk ... Jan 11 16:13:43 ... writing Suffix Array to disk ... Jan 11 16:13:43 ... writing SAindex to disk Jan 11 16:13:43 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:43 ..... started STAR run Jan 11 16:13:43 ..... loading genome Jan 11 16:13:43 ..... started mapping Jan 11 16:13:44 ..... finished mapping Jan 11 16:13:44 ..... finished successfully debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:44 ..... started STAR run Jan 11 16:13:44 ... starting to generate Genome files Jan 11 16:13:44 ..... 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 Jan 11 16:13:44 ... starting to sort Suffix Array. This may take a long time... Jan 11 16:13:44 ... sorting Suffix Array chunks and saving them to disk... Jan 11 16:13:44 ... loading chunks from disk, packing SA... Jan 11 16:13:44 ... finished generating suffix array Jan 11 16:13:44 ... generating Suffix Array index Jan 11 16:13:44 ... completed Suffix Array index Jan 11 16:13:44 ... writing Genome to disk ... Jan 11 16:13:44 ... writing Suffix Array to disk ... Jan 11 16:13:44 ... writing SAindex to disk Jan 11 16:13:44 ..... finished successfully /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 Jan 11 16:13:44 ..... started STAR run Jan 11 16:13:44 ..... loading genome Jan 11 16:13:44 ..... started mapping Jan 11 16:13:44 ..... finished mapping Jan 11 16:13:44 ..... finished successfully make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+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/reproducible-path/rna-star-2.7.10b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/bin dh_install source/STAR-avx2 source/STARlong-avx2 /usr/lib/rna-star/bin && dh_install source/STAR-avx source/STARlong-avx /usr/lib/rna-star/bin && dh_install source/STAR-sse4.1 source/STARlong-sse4.1 /usr/lib/rna-star/bin && dh_install source/STAR-ssse3 source/STARlong-ssse3 /usr/lib/rna-star/bin && dh_install source/STAR-sse3 source/STARlong-sse3 /usr/lib/rna-star/bin && dh_install source/STAR-plain source/STARlong-plain /usr/lib/rna-star/bin && true dh_install debian/bin/simd-dispatch /usr/lib/rna-star/ set -e && cd /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/bin && for prog in STAR STARlong ; do ln -s \ ../lib/rna-star/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+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/reproducible-path/rna-star-2.7.10b+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+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/reproducible-path/rna-star-2.7.10b+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' dh_md5sums -O--sourcedirectory=source dh_builddeb -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.10b+dfsg-2_amd64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rna-star_2.7.10b+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../rna-star_2.7.10b+dfsg-2_amd64.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: 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/2569962 and its subdirectories I: Current time: Thu Jan 11 04:16:45 -12 2024 I: pbuilder-time-stamp: 1704989805 Thu Jan 11 16:16:47 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Jan 11 16:16:47 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Jan 11 16:34:45 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net.