I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 7 23:00:35 -12 2025 I: pbuilder-time-stamp: 1739012435 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_2.7.8a+dfsg-2.dsc] I: copying [./rna-star_2.7.8a+dfsg.orig.tar.xz] I: copying [./rna-star_2.7.8a+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.i9jLFS7h/trustedkeys.kbx': General error gpgv: Signature made Mon Mar 1 19:15:58 2021 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.8a+dfsg-2.dsc dpkg-source: info: extracting rna-star in rna-star-2.7.8a+dfsg dpkg-source: info: unpacking rna-star_2.7.8a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.8a+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying simde.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1032865/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,-fixfilepath parallel=16 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='28af1e9e56684c5dbf7e792d25956b88' 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='1032865' 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.qWyZ2Rsz/pbuilderrc_rfRy --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qWyZ2Rsz/b1 --logfile b1/build.log rna-star_2.7.8a+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 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 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 8 15:46 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 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 5898 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 8049 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/1032865/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, vim-common, xxd, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on vim-common; however: Package vim-common is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} vim-common{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix vim vim-athena vim-gtk3 vim-nox vim-tiny wget 0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 25.6 MB of archives. After unpacking 85.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 xxd amd64 2:8.2.2434-3+deb11u1 [192 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 vim-common all 2:8.2.2434-3+deb11u1 [226 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u9 [344 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u9 [435 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2.1~deb11u1 [229 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libsimde-dev all 0.7.2-4 [259 kB] Fetched 25.6 MB in 0s (58.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package xxd. Preparing to unpack .../06-xxd_2%3a8.2.2434-3+deb11u1_amd64.deb ... Unpacking xxd (2:8.2.2434-3+deb11u1) ... Selecting previously unselected package vim-common. Preparing to unpack .../07-vim-common_2%3a8.2.2434-3+deb11u1_all.deb ... Unpacking vim-common (2:8.2.2434-3+deb11u1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../09-libmagic1_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../22-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../25-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../27-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../28-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../33-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../34-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../35-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../36-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../37-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../38-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../39-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 .../40-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../41-libcurl3-gnutls_7.74.0-1.3+deb11u9_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../42-libcurl4-gnutls-dev_7.74.0-1.3+deb11u9_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../43-libdeflate0_1.7-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.7-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../44-libdeflate-dev_1.7-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.7-1) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../45-libhts3_1.11-4_amd64.deb ... Unpacking libhts3:amd64 (1.11-4) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../46-liblzma-dev_5.2.5-2.1~deb11u1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.5-2.1~deb11u1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../47-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../48-libhts-dev_1.11-4_amd64.deb ... Unpacking libhts-dev:amd64 (1.11-4) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../49-libsimde-dev_0.7.2-4_all.deb ... Unpacking libsimde-dev (0.7.2-4) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libsimde-dev (0.7.2-4) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up xxd (2:8.2.2434-3+deb11u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up vim-common (2:8.2.2434-3+deb11u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up liblzma-dev:amd64 (5.2.5-2.1~deb11u1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libdeflate-dev:amd64 (1.7-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 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-2.7.8a+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_2.7.8a+dfsg-2_source.changes dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.8a+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' dh_autoreconf_clean -O--sourcedirectory=source dh_clean -O--sourcedirectory=source debian/rules binary dh binary --sourcedirectory=source dh_update_autotools_config -O--sourcedirectory=source dh_autoreconf -O--sourcedirectory=source dh_auto_configure -O--sourcedirectory=source debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.8a+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -std=c++11 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' samHeaders.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:41:17: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | symlink("../../../SJ.out.tab", (outputPrefixMat+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SequenceFuns.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:187:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 187 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:191:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMoutput.cpp 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 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamRemoveDuplicates.cpp 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 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' g++ -o STAR-avx -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' g++ -o STAR-sse4.1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse4.1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' g++ -o STAR-ssse3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-ssse3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' g++ -o STAR-sse3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' g++ -o STAR-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -fdebug-prefix-map=/build/reproducible-path/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/reproducible-path/rna-star-2.7.8a+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' set -i; for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.8a+dfsg/source/STAR-${SIMD} ; \ fi ; done debian/tests/run_test.sh: line 14: 1042646 Illegal instruction $1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile $ORIGDIR/foo.gtf debian/tests/run_test.sh: line 14: 1042656 Illegal instruction $1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile $ORIGDIR/foo.gtf debian/tests/run_test.sh: line 14: 1042667 Illegal instruction $1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile $ORIGDIR/foo.gtf debian/tests/run_test.sh: line 14: 1042678 Illegal instruction $1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile $ORIGDIR/foo.gtf make[1]: *** [debian/rules:53: override_dh_auto_test] Error 132 make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.8a+dfsg' make: *** [debian/rules:21: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/1032865 and its subdirectories